Variant report

Variant	rs4709485
Chromosome Location	chr6:161433981-161433982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161425971..161428615-chr6:161431158..161434140,4	K562	blood:
2	chr6:161412643..161414496-chr6:161433099..161435629,2	K562	blood:
3	chr2:194000942..194001716-chr6:161433923..161434431,2	MCF-7	breast:
4	chr6:161417175..161419433-chr6:161431394..161434552,3	K562	blood:
5	chr6:161422502..161428879-chr6:161429746..161435781,7	K562	blood:

Variant related genes	Relation type
ENSG00000272841	Chromatin interaction
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1001808	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12203648	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13200744	0.83[CHB][hapmap]
rs1534020	0.84[CEU][hapmap]
rs1562027	0.89[CHB][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2140650	0.82[EUR][1000 genomes]
rs35894036	0.85[ASN][1000 genomes]
rs3734461	0.89[CHB][hapmap];0.83[AFR][1000 genomes]
rs3757021	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4324757	0.90[CEU][hapmap]
rs4709488	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs588284	0.85[ASN][1000 genomes]
rs589238	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs590988	0.95[CHB][hapmap]
rs593184	0.85[ASN][1000 genomes]
rs594555	0.94[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs594602	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs606817	0.82[AFR][1000 genomes]
rs619831	0.84[ASN][1000 genomes]
rs625977	0.82[AFR][1000 genomes]
rs628075	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs629015	0.83[ASN][1000 genomes]
rs630006	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs630430	0.86[ASN][1000 genomes]
rs643706	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs644110	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs644486	0.82[AFR][1000 genomes]
rs645406	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs657616	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs671335	0.94[ASN][1000 genomes]
rs674220	0.85[ASN][1000 genomes]
rs675457	0.88[AFR][1000 genomes]
rs675538	0.85[ASN][1000 genomes]
rs685939	0.85[ASN][1000 genomes]
rs686392	0.85[ASN][1000 genomes]
rs686755	0.85[ASN][1000 genomes]
rs6901173	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs6901968	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs6905734	0.84[CEU][hapmap]
rs6913867	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs705826	0.82[AFR][1000 genomes]
rs7756711	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs787784	0.84[ASN][1000 genomes]
rs796835	0.85[ASN][1000 genomes]
rs9295134	0.89[CHB][hapmap];0.83[AFR][1000 genomes]
rs9347478	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9355327	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9458102	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161414200-161458200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:161414400-161469600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:161414600-161442600	Weak transcription	Primary B cells from cord blood	blood
4	chr6:161414600-161457400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:161415600-161450000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:161416600-161475200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:161416800-161436200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:161417400-161449000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:161418000-161434800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:161418000-161448800	Weak transcription	Lung	lung
11	chr6:161420000-161434800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:161422800-161434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:161422800-161441000	Weak transcription	K562	blood
14	chr6:161423000-161443000	Weak transcription	HepG2	liver
15	chr6:161423200-161436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:161428600-161455800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:161430800-161435200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:161431000-161442400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:161431200-161434200	Enhancers	Osteobl	bone
20	chr6:161431200-161434400	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr6:161431200-161434800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:161431200-161435000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:161431400-161435000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:161431600-161434000	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:161431600-161434600	Enhancers	Colon Smooth Muscle	Colon
26	chr6:161431800-161434000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:161431800-161434000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:161431800-161434000	Enhancers	Brain Hippocampus Middle	brain
29	chr6:161431800-161434000	Enhancers	Brain Substantia Nigra	brain
30	chr6:161431800-161434800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:161432000-161434000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:161432000-161438600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:161432200-161442400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:161432200-161450000	Weak transcription	HMEC	breast
35	chr6:161432200-161450400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:161432200-161451200	Weak transcription	NHEK	skin
37	chr6:161432600-161434000	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:161432600-161455400	Weak transcription	Fetal Intestine Large	intestine
39	chr6:161433000-161436200	Weak transcription	Primary T cells from cord blood	blood
40	chr6:161433000-161440400	Weak transcription	Small Intestine	intestine
41	chr6:161433000-161442400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:161433000-161449000	Weak transcription	HSMM	muscle
43	chr6:161433000-161458000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:161433200-161434000	Enhancers	Adipose Nuclei	Adipose
45	chr6:161433200-161434400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:161433200-161434600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:161433200-161434600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:161433200-161434600	Weak transcription	Pancreas	Pancrea
49	chr6:161433200-161435000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:161433200-161435200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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