Variant report

Variant	rs4975853
Chromosome Location	chr5:1818127-1818128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1816258..1819219-chr6:26198199..26201096,2	MCF-7	breast:
2	chr5:1808200..1809817-chr5:1817862..1820260,2	MCF-7	breast:
3	chr5:1814461..1816981-chr5:1818018..1821210,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197846	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11133910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133911	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11133912	0.97[ASN][1000 genomes]
rs13187162	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1845288	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873926	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242412	0.86[ASN][1000 genomes]
rs2276986	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2291944	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34233926	0.99[ASN][1000 genomes]
rs35380881	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752844	0.83[YRI][hapmap]
rs3756343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776143	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776144	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3776145	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776146	0.94[ASN][1000 genomes]
rs3776149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822364	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147769	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147770	0.96[ASN][1000 genomes]
rs4147772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975845	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4975847	0.84[JPT][hapmap]
rs4975848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883912	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6555012	0.88[ASN][1000 genomes]
rs6863367	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7702843	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs972890	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs972891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs972892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974722	0.88[CEU][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802800-1818400	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr5:1802800-1818600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:1802800-1818800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:1802800-1821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:1802800-1821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:1802800-1822000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
11	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:1803000-1818200	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:1803000-1818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:1803000-1818400	Strong transcription	NHLF	lung
18	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:1803000-1822400	Strong transcription	A549	lung
20	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
21	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr5:1803000-1822800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:1803000-1822800	Strong transcription	Osteobl	bone
24	chr5:1803000-1823800	Strong transcription	Fetal Thymus	thymus
25	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:1803000-1825600	Strong transcription	Liver	Liver
28	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
31	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
34	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:1803200-1819400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:1803200-1821800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:1803200-1822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:1803200-1823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
42	chr5:1803400-1818600	Strong transcription	Fetal Intestine Small	intestine
43	chr5:1803400-1821600	Strong transcription	Fetal Stomach	stomach
44	chr5:1803400-1822800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:1803400-1823600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:1803600-1823600	Strong transcription	Hela-S3	cervix
47	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:1803800-1822200	Strong transcription	HepG2	liver
49	chr5:1804000-1825000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:1804200-1822200	Strong transcription	Brain Germinal Matrix	brain

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