Variant report

Variant	rs10934507
Chromosome Location	chr3:119770660-119770661
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119769956..119771538-chr3:119813170..119814916,2	K562	blood:
2	chr3:119763698..119765410-chr3:119769274..119771635,2	MCF-7	breast:
3	chr3:119742589..119744639-chr3:119769517..119771054,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934500	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154595	0.85[JPT][hapmap]
rs11915717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054090	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12108149	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12630592	0.85[JPT][hapmap]
rs12630829	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632325	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12634476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12635018	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13314595	0.95[YRI][hapmap]
rs13321783	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1574154	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16830567	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16830689	0.88[YRI][hapmap]
rs1719889	0.88[YRI][hapmap]
rs1719894	0.85[JPT][hapmap]
rs17204878	0.85[JPT][hapmap]
rs1732170	0.89[JPT][hapmap]
rs1870931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980718	0.84[ASN][1000 genomes]
rs2319398	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2319399	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs28536662	0.85[JPT][hapmap]
rs28831519	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334533	0.85[JPT][hapmap]
rs334535	0.91[YRI][hapmap]
rs334559	0.87[YRI][hapmap]
rs334563	0.85[JPT][hapmap]
rs4072520	0.87[YRI][hapmap]
rs4340737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4624596	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4687890	0.85[JPT][hapmap]
rs4687893	0.86[JPT][hapmap]
rs4688042	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4688046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688053	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688054	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57939147	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58863896	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60235167	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264706	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62264708	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62264714	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62264734	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264739	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264747	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264749	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266274	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266277	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266281	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438552	0.85[JPT][hapmap]
rs6438553	0.85[JPT][hapmap]
rs6769435	0.87[YRI][hapmap]
rs6770314	0.91[YRI][hapmap]
rs6781942	0.85[JPT][hapmap]
rs6782799	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6792572	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6795653	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6797459	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6800622	0.85[JPT][hapmap]
rs6808874	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7431209	0.84[JPT][hapmap]
rs7617372	0.87[YRI][hapmap]
rs7620750	0.95[YRI][hapmap]
rs7633279	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7639388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7644234	0.85[JPT][hapmap]
rs7652172	0.91[YRI][hapmap]
rs9813864	0.89[JPT][hapmap]
rs9851174	0.91[YRI][hapmap]
rs9873477	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9878473	0.85[JPT][hapmap]
rs9879992	0.82[YRI][hapmap]

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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
2	chr3:119760000-119771200	Weak transcription	NHDF-Ad	bronchial
3	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119760200-119805400	Weak transcription	HMEC	breast
5	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119765000-119770800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:119765200-119771200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:119766200-119771800	Enhancers	Colon Smooth Muscle	Colon
9	chr3:119766400-119772200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:119766400-119772600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:119766600-119771400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:119766600-119771800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:119767200-119771600	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:119767200-119771800	Enhancers	Primary T cells from cord blood	blood
15	chr3:119767400-119771200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:119767400-119771400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:119767400-119771800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:119767400-119772400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:119767600-119772200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:119767800-119770800	Weak transcription	Fetal Kidney	kidney
21	chr3:119767800-119771200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:119768000-119771800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:119768000-119772400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:119768200-119771800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:119768200-119772200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:119768200-119772400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:119768600-119771000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:119768800-119770800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr3:119768800-119772000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
31	chr3:119769000-119771800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:119769000-119772000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:119769200-119771200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:119769200-119771200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:119769200-119771200	Weak transcription	Ovary	ovary
36	chr3:119769200-119772000	Weak transcription	Left Ventricle	heart
37	chr3:119769200-119780600	Weak transcription	Aorta	Aorta
38	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:119769400-119771800	Enhancers	NHEK	skin
40	chr3:119769600-119770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:119769600-119770800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:119769600-119770800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:119769600-119770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:119769600-119771000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:119769600-119771600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:119769600-119778400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:119769800-119770800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:119769800-119771000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:119769800-119771200	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:119769800-119771200	Weak transcription	Psoas Muscle	Psoas

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