Variant report

Variant	rs9394523
Chromosome Location	chr6:38657025-38657026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38656830..38658689-chr6:38669303..38670813,2	MCF-7	breast:
2	chr6:38654849..38657579-chr6:38658333..38661175,3	K562	blood:
3	chr6:38649077..38650795-chr6:38654620..38657310,2	K562	blood:
4	chr6:38655259..38657070-chr6:38659864..38662017,2	K562	blood:
5	chr6:38656860..38659853-chr6:38666153..38668324,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10484855	0.88[CEU][hapmap]
rs10947757	0.87[ASN][1000 genomes]
rs1130534	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13191302	0.88[CEU][hapmap]
rs13194237	0.90[EUR][1000 genomes]
rs13196530	0.88[CEU][hapmap]
rs13196708	0.88[CEU][hapmap]
rs13198900	0.88[CEU][hapmap]
rs13199033	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13203443	0.88[CEU][hapmap]
rs13209846	0.81[EUR][1000 genomes]
rs13210334	0.80[EUR][1000 genomes]
rs13212218	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13213257	0.81[EUR][1000 genomes]
rs13215896	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13217234	0.88[CEU][hapmap]
rs13218305	0.81[EUR][1000 genomes]
rs13219252	0.88[CEU][hapmap]
rs13219395	0.88[CEU][hapmap]
rs13219781	0.91[EUR][1000 genomes]
rs1579028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1621483	0.92[ASN][1000 genomes]
rs17544311	0.88[CEU][hapmap]
rs17544868	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1937782	0.81[EUR][1000 genomes]
rs34349982	0.83[EUR][1000 genomes]
rs34519749	0.81[EUR][1000 genomes]
rs34637217	0.91[EUR][1000 genomes]
rs34971977	0.85[EUR][1000 genomes]
rs35147121	0.81[EUR][1000 genomes]
rs35207097	0.83[EUR][1000 genomes]
rs35388596	0.81[EUR][1000 genomes]
rs3799703	0.92[JPT][hapmap]
rs4711553	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4711556	0.99[ASN][1000 genomes]
rs4714173	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4714174	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs57156564	0.96[ASN][1000 genomes]
rs59793635	0.84[ASN][1000 genomes]
rs60262339	0.99[ASN][1000 genomes]
rs6925790	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs6931745	0.84[ASN][1000 genomes]
rs6932648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7767791	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7775968	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9296255	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs9366969	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs9369073	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9369075	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937662	0.93[JPT][hapmap]
rs9380763	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs9394516	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9394519	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs9394522	0.98[ASN][1000 genomes]
rs9394524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462446	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9462448	0.93[JPT][hapmap]
rs9462450	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[ASN][1000 genomes]
rs9462453	0.85[ASN][1000 genomes]
rs9470901	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9470902	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs9470913	0.84[ASN][1000 genomes]
rs9470916	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9470917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9470918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs963720	0.88[CEU][hapmap]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:38641600-38668000	Weak transcription	NHLF	lung
3	chr6:38642000-38657600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:38642400-38660000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:38642400-38665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:38642800-38658000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:38646000-38670000	Weak transcription	A549	lung
9	chr6:38646600-38663400	Weak transcription	Esophagus	oesophagus
10	chr6:38646800-38668200	Weak transcription	Primary T cells from cord blood	blood
11	chr6:38647200-38659000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:38648800-38669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:38650200-38663400	Weak transcription	HUVEC	blood vessel
14	chr6:38650200-38666600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:38650800-38666400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:38651000-38667800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:38651200-38657400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:38651200-38665800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:38651200-38667800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:38651200-38668000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:38651200-38668000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:38651200-38669800	Weak transcription	HSMM	muscle
23	chr6:38651200-38670000	Weak transcription	Fetal Kidney	kidney
24	chr6:38651400-38659000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:38651400-38669400	Weak transcription	Osteobl	bone
26	chr6:38652000-38666600	Weak transcription	Fetal Intestine Small	intestine
27	chr6:38652000-38668000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:38652200-38662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:38652400-38668000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:38653000-38668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:38653000-38670000	Weak transcription	NHDF-Ad	bronchial
32	chr6:38653600-38663200	Weak transcription	HMEC	breast
33	chr6:38653600-38669400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:38653800-38663200	Weak transcription	Dnd41	blood
35	chr6:38654000-38657800	Enhancers	Liver	Liver
36	chr6:38654000-38663600	Weak transcription	K562	blood
37	chr6:38654400-38669800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:38654600-38657600	Enhancers	HepG2	liver
39	chr6:38654600-38668000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:38654600-38668000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:38654600-38668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:38654600-38669400	Weak transcription	Hela-S3	cervix
43	chr6:38655200-38657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:38655200-38662000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:38655200-38665000	Weak transcription	NHEK	skin
46	chr6:38655200-38666600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:38655200-38667400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:38655200-38669800	Weak transcription	Pancreas	Pancrea
49	chr6:38655200-38670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:38655400-38668000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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