Variant report

Variant	rs3800450
Chromosome Location	chr6:34880330-34880331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34878922..34882866-chr6:34883896..34887915,4	MCF-7	breast:
2	chr6:34874014..34875640-chr6:34878716..34880730,2	K562	blood:
3	chr6:34873430..34875640-chr6:34878874..34880730,2	K562	blood:
4	chr6:34879811..34884262-chr6:34884635..34888970,5	K562	blood:
5	chr6:34854042..34857854-chr6:34876810..34882352,6	K562	blood:

Variant related genes	Relation type
ENSG00000064995	Chromatin interaction
ENSG00000064999	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10947534	0.92[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];0.99[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[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][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[YRI][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];0.83[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];1.00[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[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][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];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800448	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800452	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]
rs3800453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][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	0.85[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];0.96[ASN][1000 genomes]
rs6913108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6918498	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[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];0.99[ASN][1000 genomes]
rs73745049	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73745050	1.00[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];0.99[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	0.90[ASN][1000 genomes]
rs847844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs847845	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847861	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs861878	0.92[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];0.98[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];0.98[ASN][1000 genomes]
rs9368837	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380465	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380466	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380468	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]
rs9380470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9380476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[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:14 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34859200-34882400	Weak transcription	Fetal Stomach	stomach
2	chr6:34859200-34884600	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:34859200-34884800	Weak transcription	Right Ventricle	heart
4	chr6:34859200-34890800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:34861600-34886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:34869600-34890000	Weak transcription	Hela-S3	cervix
7	chr6:34871800-34886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:34872400-34907200	Weak transcription	Small Intestine	intestine
9	chr6:34873200-34885400	Weak transcription	Spleen	Spleen
10	chr6:34874000-34880400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:34874200-34882400	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:34874400-34893200	Weak transcription	Fetal Intestine Large	intestine
13	chr6:34874800-34896000	Weak transcription	Brain Anterior Caudate	brain
14	chr6:34875600-34885800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:34876200-34885400	Weak transcription	Gastric	stomach
16	chr6:34876600-34880400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:34877000-34890000	Weak transcription	K562	blood
18	chr6:34877800-34881000	Weak transcription	Right Atrium	heart
19	chr6:34877800-34882600	Weak transcription	Left Ventricle	heart
20	chr6:34877800-34884800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:34877800-34892200	Weak transcription	Brain Angular Gyrus	brain
22	chr6:34877800-34921000	Weak transcription	Pancreas	Pancrea
23	chr6:34878000-34880600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr6:34878000-34885600	Weak transcription	Fetal Heart	heart
25	chr6:34878000-34891400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:34878000-34896400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:34878400-34884800	Weak transcription	Lung	lung
28	chr6:34878600-34881400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:34878800-34880400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:34879000-34881400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:34879000-34881600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:34879000-34881600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:34879200-34880400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:34879200-34880800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:34879200-34881200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:34879200-34881400	Enhancers	Primary hematopoietic stem cells	blood
37	chr6:34879200-34881400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr6:34879200-34881400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:34879200-34881600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:34879400-34881400	Enhancers	Primary T cells from cord blood	blood
41	chr6:34879400-34882400	Weak transcription	HepG2	liver
42	chr6:34879600-34880400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:34879600-34880400	Enhancers	Psoas Muscle	Psoas
44	chr6:34879600-34881400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:34879600-34881400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:34879600-34881600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:34879600-34882400	Weak transcription	Adipose Nuclei	Adipose
48	chr6:34879600-34882600	Weak transcription	Ovary	ovary
49	chr6:34879600-34884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:34879600-34885000	Weak transcription	Liver	Liver

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