Variant report

Variant	rs10080647
Chromosome Location	chr6:114742335-114742336
allele	A/C
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	TAF7	chr6:114742212-114743259	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:114742285-114743572	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr6:114742206-114742688	H1-hESC	embryonic stem cell:	n/a	chr6:114742514-114742528 chr6:114742671-114742679 chr6:114742403-114742417 chr6:114742509-114742523
4	POLR2A	chr6:114738997-114744004	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:114742313-114742680	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr6:114742198-114742792	H1-hESC	embryonic stem cell:	n/a	n/a
7	NANOG	chr6:114742260-114742779	H1-hESC	embryonic stem cell:	n/a	chr6:114742528-114742537
8	ATF2	chr6:114742313-114742815	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr6:114742330-114742679	H1-hESC	embryonic stem cell:	n/a	chr6:114742480-114742489 chr6:114742404-114742418
10	SP1	chr6:114742280-114742712	H1-hESC	embryonic stem cell:	n/a	chr6:114742424-114742438
11	CHD1	chr6:114741717-114742852	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:114742149-114743333	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:114742195-114743304	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr6:114742322-114742801	H1-hESC	embryonic stem cell:	n/a	chr6:114742424-114742438
15	ATF2	chr6:114742286-114742964	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr6:114742260-114742596	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr6:114742335-114742740	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000228624	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10155706	0.92[AFR][1000 genomes]
rs10155761	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1033885	0.94[JPT][hapmap]
rs10872117	0.80[ASN][1000 genomes]
rs11153481	0.81[ASN][1000 genomes]
rs11962755	0.96[ASN][1000 genomes]
rs11964902	0.83[ASN][1000 genomes]
rs11965041	0.83[ASN][1000 genomes]
rs11968668	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12194487	0.85[ASN][1000 genomes]
rs1323046	0.80[ASN][1000 genomes]
rs1323047	0.83[ASN][1000 genomes]
rs1323048	0.80[ASN][1000 genomes]
rs1324441	0.94[JPT][hapmap]
rs1324446	0.84[ASN][1000 genomes]
rs1324447	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1337330	0.84[ASN][1000 genomes]
rs1337335	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337336	0.95[ASN][1000 genomes]
rs1407729	0.83[ASN][1000 genomes]
rs1408452	0.88[JPT][hapmap]
rs1408453	0.88[JPT][hapmap]
rs1408454	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.84[ASN][1000 genomes]
rs1415428	0.80[ASN][1000 genomes]
rs1415429	0.80[ASN][1000 genomes]
rs1415430	0.80[ASN][1000 genomes]
rs17326650	0.96[ASN][1000 genomes]
rs1856118	0.90[ASN][1000 genomes]
rs2205734	0.81[ASN][1000 genomes]
rs2205737	0.96[ASN][1000 genomes]
rs2224692	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2281012	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2294232	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2349468	0.96[ASN][1000 genomes]
rs2882172	0.96[ASN][1000 genomes]
rs4945515	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.84[ASN][1000 genomes]
rs4945998	0.82[ASN][1000 genomes]
rs4946001	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.84[ASN][1000 genomes]
rs4946003	0.82[JPT][hapmap]
rs56067384	0.96[ASN][1000 genomes]
rs6568838	0.82[ASN][1000 genomes]
rs6568839	0.84[ASN][1000 genomes]
rs6900066	0.81[YRI][hapmap]
rs6902333	0.86[ASN][1000 genomes]
rs6902384	0.86[ASN][1000 genomes]
rs6917878	0.80[ASN][1000 genomes]
rs6919491	0.96[ASN][1000 genomes]
rs6926249	0.96[ASN][1000 genomes]
rs748420	0.81[GIH][hapmap]
rs7749363	0.96[ASN][1000 genomes]
rs7754407	0.84[ASN][1000 genomes]
rs9320491	0.96[ASN][1000 genomes]
rs9320493	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9374461	0.86[ASN][1000 genomes]
rs9374463	0.84[ASN][1000 genomes]
rs9481441	0.81[ASN][1000 genomes]
rs9488377	0.81[YRI][hapmap]
rs9488389	0.85[ASN][1000 genomes]
rs9488390	1.00[ASN][1000 genomes]
rs9488391	0.96[ASN][1000 genomes]
rs9488397	0.95[ASN][1000 genomes]
rs9488398	0.86[AFR][1000 genomes]
rs9488404	0.83[JPT][hapmap]
rs9688943	0.83[JPT][hapmap]
rs969877	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv604544	chr6:114489321-114837181	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' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv428494	chr6:114666307-114774841	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2758074	chr6:114666308-115526957	Enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1030191	chr6:114679497-115228028	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv538424	chr6:114679497-115228028	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1025817	chr6:114715204-115006108	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10080647	RWDD1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114740200-114743400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:114740400-114743400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:114740600-114745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:114740600-114751800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:114741200-114743200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:114741400-114743400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:114741600-114742400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:114741800-114743600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
9	chr6:114742000-114742400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr6:114742000-114742400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:114742000-114742400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:114742000-114743600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
13	chr6:114742200-114742400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:114742200-114743200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:114742200-114743600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:114742200-114744000	Active TSS	H9 Cell Line	embryonic stem cell

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