Variant report

Variant	rs7753949
Chromosome Location	chr6:34882394-34882395
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	chr6:34882380..34884739-chr6:34891230..34893297,2	MCF-7	breast:
3	chr6:34879811..34884262-chr6:34884635..34888970,5	K562	blood:
4	chr6:34880699..34884444-chr6:34885944..34888970,5	K562	blood:
5	chr6:34855097..34857229-chr6:34880409..34882813,2	K562	blood:

Variant related genes	Relation type
ENSG00000064995	Chromatin interaction
ENSG00000064999	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10947536	0.91[GIH][hapmap]
rs11969436	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13219624	0.85[GIH][hapmap]
rs1535001	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1737727	0.91[GIH][hapmap]
rs1996912	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2140418	0.91[GIH][hapmap]
rs2177381	0.91[GIH][hapmap]
rs2273006	0.82[GIH][hapmap]
rs2293242	0.91[GIH][hapmap]
rs2473615	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2820237	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs2985	0.82[GIH][hapmap]
rs3817473	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4646926	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646949	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6912327	0.86[CEU][hapmap]
rs847846	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs847848	0.80[GIH][hapmap]
rs847850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs847851	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs847852	0.85[JPT][hapmap]
rs847859	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296139	0.85[GIH][hapmap]
rs9380469	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9394248	0.85[CHB][hapmap];0.84[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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7753949	C6orf89	cis	parietal	SCAN
rs7753949	UHRF1BP1	cis	parietal	SCAN
rs7753949	UHRF1BP1	cis	Artery Tibial	GTEx
rs7753949	UHRF1BP1	cis	Adipose Subcutaneous	GTEx
rs7753949	TAF11	cis	parietal	SCAN
rs7753949	PRDM7	trans	multi-tissue	Pritchard
rs7753949	UHRF1BP1	cis	Muscle Skeletal	GTEx
rs7753949	TAF11	cis	lymphoblastoid	seeQTL
rs7753949	UHRF1BP1	cis	Esophagus Muscularis	GTEx
rs7753949	TAF11	cis	cerebellum	SCAN

Chromatin state (count:72 , 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	chr6:34874200-34882400	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:34874400-34893200	Weak transcription	Fetal Intestine Large	intestine
12	chr6:34874800-34896000	Weak transcription	Brain Anterior Caudate	brain
13	chr6:34875600-34885800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:34876200-34885400	Weak transcription	Gastric	stomach
15	chr6:34877000-34890000	Weak transcription	K562	blood
16	chr6:34877800-34882600	Weak transcription	Left Ventricle	heart
17	chr6:34877800-34884800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:34877800-34892200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:34877800-34921000	Weak transcription	Pancreas	Pancrea
20	chr6:34878000-34885600	Weak transcription	Fetal Heart	heart
21	chr6:34878000-34891400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:34878000-34896400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:34878400-34884800	Weak transcription	Lung	lung
24	chr6:34879400-34882400	Weak transcription	HepG2	liver
25	chr6:34879600-34882400	Weak transcription	Adipose Nuclei	Adipose
26	chr6:34879600-34882600	Weak transcription	Ovary	ovary
27	chr6:34879600-34884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:34879600-34885000	Weak transcription	Liver	Liver
29	chr6:34879600-34886000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:34879600-34892200	Weak transcription	Fetal Intestine Small	intestine
31	chr6:34879600-34892200	Weak transcription	Fetal Kidney	kidney
32	chr6:34879600-34893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:34879600-34896800	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:34879800-34891800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:34879800-34893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:34880000-34883200	Enhancers	HUVEC	blood vessel
37	chr6:34880000-34888800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:34880400-34882600	Weak transcription	Psoas Muscle	Psoas
39	chr6:34880400-34884200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:34880400-34884600	Weak transcription	Aorta	Aorta
41	chr6:34880800-34893400	Weak transcription	Fetal Thymus	thymus
42	chr6:34881000-34883600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:34881000-34889200	Weak transcription	Primary B cells from cord blood	blood
44	chr6:34881000-34898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:34881200-34882600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:34881200-34884000	Weak transcription	NHDF-Ad	bronchial
47	chr6:34881200-34885400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:34881200-34887200	Weak transcription	NHEK	skin
49	chr6:34881200-34890200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:34881200-34893000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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