Variant report

Variant	rs2814965
Chromosome Location	chr6:34711946-34711947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:34711880-34712357	H1-hESC	embryonic stem cell:	n/a	n/a
2	HEY1	chr6:34711878-34712277	K562	blood:	n/a	chr6:34711924-34711939
3	ZBTB33	chr6:34711768-34712345	K562	blood:	n/a	n/a
4	POLR2A	chr6:34711893-34712322	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000217130	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1125342	0.87[ASN][1000 genomes]
rs16894102	0.94[ASN][1000 genomes]
rs16894945	0.84[ASN][1000 genomes]
rs16894995	0.84[ASN][1000 genomes]
rs2064253	0.80[EUR][1000 genomes]
rs2236392	0.94[ASN][1000 genomes]
rs2744948	0.81[EUR][1000 genomes]
rs2744953	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2764199	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764200	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2764202	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814954	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2815003	0.81[EUR][1000 genomes]
rs3734260	0.82[ASN][1000 genomes]
rs3734263	0.81[ASN][1000 genomes]
rs3736896	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777751	0.88[ASN][1000 genomes]
rs3798349	0.88[ASN][1000 genomes]
rs3798351	0.94[ASN][1000 genomes]
rs3800455	0.91[ASN][1000 genomes]
rs3800456	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41438444	0.87[ASN][1000 genomes]
rs4443503	0.80[ASN][1000 genomes]
rs4711399	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713823	0.83[ASN][1000 genomes]
rs56825685	0.83[ASN][1000 genomes]
rs56842618	0.95[ASN][1000 genomes]
rs57338415	0.83[ASN][1000 genomes]
rs57637041	0.82[ASN][1000 genomes]
rs57645599	0.91[ASN][1000 genomes]
rs57916801	0.94[ASN][1000 genomes]
rs58654146	0.88[ASN][1000 genomes]
rs58817410	0.88[ASN][1000 genomes]
rs58833137	0.83[ASN][1000 genomes]
rs59014029	0.94[ASN][1000 genomes]
rs59851773	0.88[ASN][1000 genomes]
rs59884600	0.94[ASN][1000 genomes]
rs59952325	0.88[ASN][1000 genomes]
rs60410089	0.95[ASN][1000 genomes]
rs60439875	0.85[ASN][1000 genomes]
rs60754257	0.91[ASN][1000 genomes]
rs6906500	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932930	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939345	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73413893	0.89[ASN][1000 genomes]
rs73415706	0.98[ASN][1000 genomes]
rs73415742	0.97[ASN][1000 genomes]
rs73415758	0.98[ASN][1000 genomes]
rs73415760	0.98[ASN][1000 genomes]
rs73415779	0.94[ASN][1000 genomes]
rs73415781	0.95[ASN][1000 genomes]
rs73417752	0.89[ASN][1000 genomes]
rs73417786	0.89[ASN][1000 genomes]
rs73419615	0.88[ASN][1000 genomes]
rs73419643	0.84[ASN][1000 genomes]
rs73419650	0.82[ASN][1000 genomes]
rs73419656	0.83[ASN][1000 genomes]
rs73419658	0.83[ASN][1000 genomes]
rs73419660	0.83[ASN][1000 genomes]
rs73419689	0.83[ASN][1000 genomes]
rs7739335	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7751664	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7752237	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7772600	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296126	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368829	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380451	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking 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 lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
5	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
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	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
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv885795	chr6:34704613-34823187	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv965713	chr6:34708188-34713851	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2814965	SNRPC	Cis_1M	lymphoblastoid	RTeQTL
rs2814965	UHRF1BP1	cis	Artery Tibial	GTEx
rs2814965	UHRF1BP1	cis	Whole Blood	GTEx
rs2814965	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2814965	UHRF1BP1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34698000-34714000	Weak transcription	Esophagus	oesophagus
2	chr6:34699800-34712200	Weak transcription	Stomach Mucosa	stomach
3	chr6:34706400-34712800	Enhancers	HepG2	liver
4	chr6:34708400-34712800	Weak transcription	A549	lung
5	chr6:34708600-34712200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:34708600-34712200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:34708600-34712600	Weak transcription	Hela-S3	cervix
8	chr6:34708600-34713000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:34708600-34713200	Weak transcription	Liver	Liver
10	chr6:34709000-34712800	Weak transcription	K562	blood
11	chr6:34709400-34712200	Weak transcription	Small Intestine	intestine
12	chr6:34711200-34712800	Enhancers	NHEK	skin
13	chr6:34711200-34713200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:34711200-34713200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:34711400-34714600	Enhancers	Placenta	Placenta
16	chr6:34711600-34712000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr6:34711600-34712600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:34711600-34715400	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links