Variant report

Variant	rs9380468
Chromosome Location	chr6:34873814-34873815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34853843..34858855-chr6:34871881..34876120,6	MCF-7	breast:
2	chr6:34856018..34858760-chr6:34873113..34875329,3	K562	blood:
3	chr6:34873430..34875640-chr6:34878874..34880730,2	K562	blood:

Variant related genes	Relation type
ENSG00000064999	Chromatin interaction
ENSG00000064995	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10947534	0.93[JPT][hapmap]
rs10947535	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11755713	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs13204222	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13220916	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16895035	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16895354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1737724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1883639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030611	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2395601	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs34006431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35057781	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35499928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35760768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35786848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734258	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3734259	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777750	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs3800443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800448	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800453	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4646919	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646920	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646941	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140217	0.83[ASN][1000 genomes]
rs57955553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58595551	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6457799	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6907427	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912229	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6918498	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6927009	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936820	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941065	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73745049	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73745050	0.98[ASN][1000 genomes]
rs7740148	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7751820	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7752468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7755801	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs847842	0.88[ASN][1000 genomes]
rs847844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs847845	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs847861	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs847862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs861878	0.90[ASN][1000 genomes]
rs9357185	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357187	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366870	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368835	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368837	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9380476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394256	0.87[AFR][1000 genomes]
rs9784889	0.93[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv870010	chr6:34713359-34880048	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1025374	chr6:34723723-34887316	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv462905	chr6:34728253-34886436	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv602906	chr6:34728253-34886436	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1015792	chr6:34741917-34887316	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv1021733	chr6:34751052-34887316	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
15	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
16	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34858000-34877600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:34858400-34877400	Weak transcription	Aorta	Aorta
3	chr6:34858600-34879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:34858800-34880200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:34859000-34874000	Weak transcription	Brain Anterior Caudate	brain
6	chr6:34859000-34875200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:34859000-34879600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:34859200-34874800	Weak transcription	K562	blood
9	chr6:34859200-34876800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:34859200-34879000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:34859200-34882400	Weak transcription	Fetal Stomach	stomach
12	chr6:34859200-34884600	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:34859200-34884800	Weak transcription	Right Ventricle	heart
14	chr6:34859200-34890800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:34859400-34879400	Weak transcription	Primary T cells from cord blood	blood
16	chr6:34859400-34880200	Weak transcription	Primary B cells from cord blood	blood
17	chr6:34860000-34876000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:34860200-34879600	Weak transcription	Psoas Muscle	Psoas
19	chr6:34861000-34880000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:34861200-34880000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:34861600-34886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:34863200-34879200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:34863400-34877600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:34868400-34876000	Weak transcription	Pancreas	Pancrea
25	chr6:34869000-34879000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:34869400-34878800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:34869600-34890000	Weak transcription	Hela-S3	cervix
28	chr6:34869800-34879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:34870200-34877600	Weak transcription	Lung	lung
30	chr6:34870600-34877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:34871600-34874600	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:34871800-34886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:34872400-34876000	Weak transcription	Fetal Heart	heart
34	chr6:34872400-34907200	Weak transcription	Small Intestine	intestine
35	chr6:34872600-34874400	Enhancers	Fetal Intestine Large	intestine
36	chr6:34872800-34874000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:34872800-34874200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:34872800-34874200	Genic enhancers	Fetal Intestine Small	intestine
39	chr6:34872800-34880200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:34873000-34874200	Enhancers	Adipose Nuclei	Adipose
41	chr6:34873200-34875800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:34873200-34878600	Weak transcription	HepG2	liver
43	chr6:34873200-34885400	Weak transcription	Spleen	Spleen
44	chr6:34873400-34874200	Enhancers	Colon Smooth Muscle	Colon
45	chr6:34873400-34876600	Enhancers	Stomach Mucosa	stomach
46	chr6:34873600-34874200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:34873600-34874200	Enhancers	Gastric	stomach
48	chr6:34873600-34874200	Enhancers	Right Atrium	heart
49	chr6:34873600-34874800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:34873600-34875000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links