Variant report

Variant	rs6544173
Chromosome Location	chr2:38959427-38959428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38958596..38960601-chr2:38963108..38966299,3	K562	blood:
2	chr2:38957599..38960532-chr2:38963906..38966818,3	MCF-7	breast:
3	chr2:38828482..38830081-chr2:38959059..38962249,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11124646	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1138974	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1138975	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13011311	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1997377	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2272445	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731838	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670891	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728394	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6731386	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6736004	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6746818	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756847	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7581263	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7581653	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7596239	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7603676	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7603821	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7604054	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7604132	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:57 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1797820	chr2:38941956-38972456	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv820974	chr2:38945458-38972971	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv1814150	chr2:38948483-38972456	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv1795154	chr2:38951608-38971432	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv1800732	chr2:38951608-38973837	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
8	esv1791751	chr2:38953669-38968842	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv2763640	chr2:38954419-38977371	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases
10	esv1837294	chr2:38955129-38965076	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv581486	chr2:38955129-38971745	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv819664	chr2:38955537-38972936	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
13	esv1796087	chr2:38955665-38969042	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	esv1796733	chr2:38955665-38969042	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	esv1807919	chr2:38955665-38969042	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	esv1809603	chr2:38955665-38969042	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	esv1817201	chr2:38955665-38969042	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
18	esv1818810	chr2:38955665-38969042	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
19	esv1833004	chr2:38955665-38969042	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
20	esv1833314	chr2:38955665-38969042	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
21	esv1843703	chr2:38955665-38969042	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
22	esv1845006	chr2:38955665-38969042	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
23	nsv828997	chr2:38955665-38972971	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
24	esv1834061	chr2:38955862-38972281	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
25	esv1839313	chr2:38955862-38972281	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
26	nsv441752	chr2:38955862-38972281	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
27	esv1792928	chr2:38955865-38968842	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
28	esv1812013	chr2:38955865-38968842	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
29	esv1812402	chr2:38955865-38968842	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
30	esv1819373	chr2:38955865-38968842	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
31	esv1819586	chr2:38955865-38968842	Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
32	esv1830555	chr2:38955865-38968842	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
33	esv1832327	chr2:38955865-38968842	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
34	esv1844402	chr2:38955865-38968842	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
35	esv1848077	chr2:38955865-38968842	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
36	esv1820680	chr2:38955865-38973046	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
37	esv1831489	chr2:38955865-38973046	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
38	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
39	esv1835023	chr2:38955866-38972281	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
40	esv2421335	chr2:38955866-38972281	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
41	esv20771	chr2:38955877-38972830	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
42	nsv581487	chr2:38955977-38964531	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
43	esv1838209	chr2:38955977-38965076	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
44	esv1838772	chr2:38955977-38965076	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
45	esv1838931	chr2:38955977-38965076	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
46	esv1840577	chr2:38955977-38965076	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
47	nsv581488	chr2:38955977-38970130	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
48	nsv581489	chr2:38955977-38970979	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
49	nsv581490	chr2:38955977-38973814	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
50	esv1834132	chr2:38955977-38977612	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544173	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
4	chr2:38930600-38965000	Weak transcription	Gastric	stomach
5	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
7	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:38948200-38968200	Weak transcription	Stomach Mucosa	stomach
9	chr2:38948400-38964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:38948400-38964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:38948400-38970600	Weak transcription	NHEK	skin
12	chr2:38948600-38959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:38948600-38970200	Weak transcription	NHDF-Ad	bronchial
14	chr2:38948600-38971200	Weak transcription	Fetal Kidney	kidney
15	chr2:38948800-38960200	Weak transcription	Hela-S3	cervix
16	chr2:38948800-38960600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:38948800-38964600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:38949000-38965000	Weak transcription	Right Ventricle	heart
19	chr2:38950000-38964600	Weak transcription	HUVEC	blood vessel
20	chr2:38950200-38970400	Weak transcription	Right Atrium	heart
21	chr2:38950400-38960400	Weak transcription	Pancreas	Pancrea
22	chr2:38950400-38970400	Weak transcription	Psoas Muscle	Psoas
23	chr2:38950400-38973600	Weak transcription	Fetal Brain Male	brain
24	chr2:38950600-38960200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:38950600-38960400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:38950600-38960600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:38950800-38964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:38950800-38964600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:38950800-38965000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:38950800-38969600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:38950800-38972200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:38951000-38970600	Weak transcription	Fetal Heart	heart
33	chr2:38953200-38964600	Weak transcription	K562	blood
34	chr2:38953400-38960200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:38954000-38964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:38954400-38960400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:38954400-38960400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:38955800-38960200	Weak transcription	Dnd41	blood
39	chr2:38955800-38961400	Strong transcription	Fetal Intestine Large	intestine
40	chr2:38956000-38961200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:38956000-38961800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:38956000-38962400	Strong transcription	Primary T cells from cord blood	blood
43	chr2:38956000-38962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:38956000-38962600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:38956000-38962600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:38956000-38962800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:38956400-38962000	Strong transcription	Fetal Intestine Small	intestine
48	chr2:38956400-38962600	Strong transcription	Fetal Stomach	stomach
49	chr2:38956400-38963200	Strong transcription	Thymus	Thymus
50	chr2:38956600-38960800	Strong transcription	Adipose Nuclei	Adipose

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