Variant report

Variant	rs10934505
Chromosome Location	chr3:119767322-119767323
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119765292..119768147-chr3:119813625..119815226,2	K562	blood:
2	chr3:119766647..119769158-chr3:119813625..119815410,2	K562	blood:
3	chr3:119766726..119769523-chr3:119811543..119814551,3	MCF-7	breast:
4	chr3:119766444..119768351-chr3:119810376..119812777,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

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];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934500	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];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];0.83[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];0.88[EUR][1000 genomes];0.94[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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934507	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]
rs1154595	0.87[JPT][hapmap]
rs11915717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12053912	0.82[CEU][hapmap]
rs12054090	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12108149	0.95[AFR][1000 genomes];0.95[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	0.87[JPT][hapmap]
rs12630829	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632325	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12635018	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13314595	0.89[YRI][hapmap]
rs13321783	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1574154	1.00[CEU][hapmap];0.91[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	0.84[YRI][hapmap]
rs16830730	0.82[CEU][hapmap]
rs1719889	0.90[YRI][hapmap]
rs1719894	0.87[JPT][hapmap]
rs17204878	0.87[JPT][hapmap]
rs1732170	0.91[JPT][hapmap]
rs1870931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980718	0.84[ASN][1000 genomes]
rs2199503	0.82[JPT][hapmap]
rs2319398	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2319399	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs28536662	0.87[JPT][hapmap]
rs28831519	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334533	0.87[JPT][hapmap]
rs334535	0.92[YRI][hapmap]
rs334559	0.82[YRI][hapmap]
rs334563	0.87[JPT][hapmap]
rs4072520	0.82[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];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4687890	0.87[JPT][hapmap]
rs4687893	0.87[JPT][hapmap]
rs4688042	1.00[CEU][hapmap];0.91[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];0.84[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];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688053	0.84[AFR][1000 genomes];0.89[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];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60235167	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[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];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264739	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264747	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264749	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266274	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266277	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266281	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438552	0.87[JPT][hapmap]
rs6438553	0.87[JPT][hapmap]
rs6769435	0.82[YRI][hapmap]
rs6770314	0.92[YRI][hapmap]
rs6781942	0.87[JPT][hapmap]
rs6782799	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6792572	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6795653	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6797459	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800622	0.87[JPT][hapmap]
rs6808874	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7431209	0.86[JPT][hapmap]
rs7617372	0.89[YRI][hapmap]
rs7620750	0.89[YRI][hapmap]
rs7633279	0.91[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];0.96[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7644234	0.87[JPT][hapmap]
rs7652172	0.85[YRI][hapmap]
rs9813864	0.91[JPT][hapmap]
rs9851174	0.92[YRI][hapmap]
rs9873477	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9878473	0.87[JPT][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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119757800-119769800	ZNF genes & repeats	Dnd41	blood
2	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
3	chr3:119760000-119770200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:119760000-119771200	Weak transcription	NHDF-Ad	bronchial
5	chr3:119760200-119767400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:119760200-119767400	Weak transcription	Right Ventricle	heart
7	chr3:119760200-119768200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:119760200-119768600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:119760200-119768800	Weak transcription	Ovary	ovary
10	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:119760200-119805400	Weak transcription	HMEC	breast
12	chr3:119760800-119767400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:119761200-119769200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:119761400-119768000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:119761600-119768200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:119763200-119769600	Weak transcription	Gastric	stomach
17	chr3:119764400-119769800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:119764600-119768800	Weak transcription	Aorta	Aorta
19	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:119764800-119767400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:119764800-119768000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:119764800-119768200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:119764800-119769400	Weak transcription	Fetal Lung	lung
24	chr3:119765000-119767400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:119765000-119768400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:119765000-119769000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:119765000-119770800	Weak transcription	Primary B cells from cord blood	blood
28	chr3:119765200-119768400	Weak transcription	Fetal Brain Female	brain
29	chr3:119765200-119771200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:119765600-119769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:119766200-119771800	Enhancers	Colon Smooth Muscle	Colon
32	chr3:119766400-119769000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:119766400-119769200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:119766400-119769200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:119766400-119769400	Weak transcription	NHEK	skin
36	chr3:119766400-119772200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:119766400-119772600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:119766600-119767400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:119766600-119771400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:119766600-119771800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr3:119766800-119767400	Weak transcription	Brain Substantia Nigra	brain
42	chr3:119766800-119767400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:119766800-119768200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:119766800-119768600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:119766800-119769000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:119766800-119769200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:119766800-119770000	Enhancers	Brain Angular Gyrus	brain
48	chr3:119767000-119767400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:119767000-119770400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:119767200-119767400	Enhancers	Psoas Muscle	Psoas

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