Variant report

Variant	rs6781942
Chromosome Location	chr3:119758049-119758050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119758032-119758183	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119754878..119758165-chr3:119760689..119763266,3	MCF-7	breast:
2	chr3:119756140..119758480-chr3:119764855..119767283,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241546	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10433404	0.87[JPT][hapmap]
rs10934500	0.87[JPT][hapmap]
rs10934502	0.87[JPT][hapmap]
rs10934503	0.86[JPT][hapmap]
rs10934505	0.87[JPT][hapmap]
rs10934506	0.87[JPT][hapmap]
rs10934507	0.85[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11915717	0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.87[JPT][hapmap]
rs12630592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.87[JPT][hapmap]
rs12638973	0.86[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1546753	0.80[AMR][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1719890	0.82[ASN][1000 genomes]
rs1719891	0.81[ASN][1000 genomes]
rs1719894	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17204878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732168	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1732170	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17810676	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870931	0.87[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126583	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2319399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs28536662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3107669	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs334533	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334553	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334564	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340737	0.87[JPT][hapmap]
rs4491945	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4624596	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687892	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688042	0.87[JPT][hapmap]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs57695730	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58605236	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438552	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6792572	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6795653	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6796420	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800622	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6805251	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6808975	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.87[JPT][hapmap]
rs7639388	0.91[JPT][hapmap]
rs7641045	0.82[ASN][1000 genomes]
rs7643875	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813864	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9866394	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873477	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9878473	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9879295	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119740000-119758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:119741200-119758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:119744400-119758400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119745200-119758400	Weak transcription	HepG2	liver
5	chr3:119745400-119758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:119747600-119758400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:119747800-119758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:119749000-119758400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:119750400-119758400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:119751800-119766800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:119753400-119758200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:119754200-119758400	Weak transcription	Thymus	Thymus
13	chr3:119756200-119758400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:119756400-119758400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:119756600-119758200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:119756800-119758200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:119757000-119760000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr3:119757000-119760800	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr3:119757000-119765000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr3:119757200-119758800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
21	chr3:119757200-119760800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:119757200-119761200	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr3:119757200-119763200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr3:119757200-119765800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:119757400-119758200	Weak transcription	A549	lung
26	chr3:119757400-119758400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:119757400-119758400	Weak transcription	Esophagus	oesophagus
28	chr3:119757400-119758400	Weak transcription	Lung	lung
29	chr3:119757400-119758600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:119757400-119760400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
31	chr3:119757400-119762400	Weak transcription	Pancreas	Pancrea
32	chr3:119757600-119758600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:119757800-119758200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:119757800-119759200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:119757800-119759600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:119757800-119760000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr3:119757800-119760400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:119757800-119760800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:119757800-119769800	ZNF genes & repeats	Dnd41	blood
40	chr3:119758000-119758800	ZNF genes & repeats	HSMM	muscle
41	chr3:119758000-119759000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr3:119758000-119759600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr3:119758000-119759800	ZNF genes & repeats	Fetal Lung	lung
44	chr3:119758000-119760000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr3:119758000-119760000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr3:119758000-119760000	ZNF genes & repeats	NHDF-Ad	bronchial
47	chr3:119758000-119760200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:119758000-119760200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:119758000-119760200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr3:119758000-119760200	ZNF genes & repeats	Fetal Intestine Small	intestine

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