Variant report

Variant	rs9784393
Chromosome Location	chr3:119556346-119556347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119554755..119557053-chr3:119812364..119815770,3	MCF-7	breast:
2	chr3:119549554..119552189-chr3:119554613..119556599,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1154597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13312998	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13314595	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs1626696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16830683	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1719887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1719888	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1732165	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1732169	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037547	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2461827	0.88[ASN][1000 genomes]
rs3108749	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3853592	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4072520	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs4438691	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4605584	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60272712	0.85[EUR][1000 genomes]
rs6438550	0.90[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66650215	0.82[ASN][1000 genomes]
rs6762640	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6769435	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs6770314	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs6771023	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6790751	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs6797689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6797879	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6807868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7617372	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs7620750	1.00[CHD][hapmap]
rs7624540	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7628426	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7635604	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7650554	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9829763	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs9851174	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs9879992	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
3	chr3:119534800-119558600	Weak transcription	Colonic Mucosa	Colon
4	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
5	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119539000-119576400	Weak transcription	Ovary	ovary
9	chr3:119540400-119563600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:119540400-119574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:119540400-119576600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:119540800-119577000	Weak transcription	Aorta	Aorta
13	chr3:119541000-119581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:119541200-119561800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:119541200-119587000	Weak transcription	Gastric	stomach
16	chr3:119541800-119559200	Weak transcription	Pancreas	Pancrea
17	chr3:119541800-119560000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:119542400-119581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:119542600-119560800	Weak transcription	Hela-S3	cervix
20	chr3:119542600-119581600	Weak transcription	HUVEC	blood vessel
21	chr3:119542800-119575000	Weak transcription	Fetal Kidney	kidney
22	chr3:119544000-119561800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:119545000-119559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:119545000-119576400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:119545200-119559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:119545200-119559400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:119545200-119561600	Weak transcription	Fetal Stomach	stomach
28	chr3:119545200-119562800	Weak transcription	NHLF	lung
29	chr3:119545200-119575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:119545200-119575000	Weak transcription	Adipose Nuclei	Adipose
31	chr3:119545200-119575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:119545200-119583400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:119545800-119560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:119545800-119576400	Weak transcription	Brain Germinal Matrix	brain
35	chr3:119545800-119581600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:119546000-119558200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:119546000-119558200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:119546000-119561800	Weak transcription	Left Ventricle	heart
39	chr3:119546000-119561800	Weak transcription	Thymus	Thymus
40	chr3:119546000-119569000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:119546000-119571800	Weak transcription	GM12878-XiMat	blood
42	chr3:119546000-119575000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:119546000-119576400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:119546000-119663400	Weak transcription	Lung	lung
45	chr3:119546200-119559400	Weak transcription	Fetal Thymus	thymus
46	chr3:119546200-119561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:119546200-119569000	Weak transcription	Placenta	Placenta
48	chr3:119546200-119575000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:119546400-119556800	Weak transcription	NHEK	skin
50	chr3:119546400-119557000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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