Variant report

Variant	rs1265351
Chromosome Location	chr6:5080904-5080905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:5080747-5081209	HepG2	liver:	n/a	n/a
2	FOSL2	chr6:5080837-5081220	HepG2	liver:	n/a	n/a
3	SMC3	chr6:5080855-5081425	HepG2	liver:	n/a	n/a
4	HEY1	chr6:5080827-5081791	HepG2	liver:	n/a	n/a
5	MYBL2	chr6:5080601-5081588	HepG2	liver:	n/a	n/a
6	MYBL2	chr6:5080726-5081693	HepG2	liver:	n/a	n/a
7	JUN	chr6:5080524-5081202	HepG2	liver:	n/a	n/a
8	ARID3A	chr6:5080593-5081453	HepG2	liver:	n/a	n/a
9	FOXA2	chr6:5080777-5081508	HepG2	liver:	n/a	n/a
10	TEAD4	chr6:5080400-5081451	HepG2	liver:	n/a	n/a
11	RCOR1	chr6:5080768-5081421	HepG2	liver:	n/a	n/a
12	MXI1	chr6:5080567-5081684	HepG2	liver:	n/a	n/a
13	FOXA1	chr6:5080802-5081548	HepG2	liver:	n/a	n/a
14	FOXA1	chr6:5080726-5081529	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:5080171..5082939-chr6:5089292..5092079,2	MCF-7	breast:
2	chr6:5079785..5081381-chr6:5089374..5091355,2	MCF-7	breast:
3	chr6:5072255..5076149-chr6:5080723..5083422,4	K562	blood:
4	chr6:5079080..5082683-chr6:5086665..5090602,4	K562	blood:

No data

Variant related genes	Relation type
PPP1R3G	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11242988	0.82[JPT][hapmap]
rs1265347	0.96[ASN][1000 genomes]
rs13340416	0.81[ASN][1000 genomes]
rs200852	0.91[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200853	0.91[CHD][hapmap];0.90[MEX][hapmap]
rs200854	0.91[CHD][hapmap];0.85[MEX][hapmap]
rs200856	0.91[CHD][hapmap];0.90[MEX][hapmap]
rs374283	0.81[ASN][1000 genomes]
rs376210	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs378259	0.81[ASN][1000 genomes]
rs379169	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398302	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421273	0.81[ASN][1000 genomes]
rs425133	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441144	0.96[ASN][1000 genomes]
rs449288	0.96[ASN][1000 genomes]
rs450634	0.96[ASN][1000 genomes]
rs7752352	0.96[ASN][1000 genomes]
rs7752365	0.90[ASN][1000 genomes]
rs9378416	0.81[ASN][1000 genomes]
rs9378928	0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs9378930	0.81[ASN][1000 genomes]
rs9378931	0.81[ASN][1000 genomes]
rs9378932	0.94[ASN][1000 genomes]
rs9378933	0.96[ASN][1000 genomes]
rs9392071	0.96[ASN][1000 genomes]
rs9392650	0.91[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9392651	0.96[ASN][1000 genomes]
rs9392653	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9405254	0.91[CHD][hapmap]
rs9405256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1024028	chr6:5057399-5081990	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
12	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1265351	LYRM4	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5071800-5082400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5074200-5081600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:5075400-5082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:5077600-5082800	Weak transcription	Spleen	Spleen
5	chr6:5080000-5084800	Enhancers	NHDF-Ad	bronchial
6	chr6:5080400-5085400	Flanking Active TSS	HepG2	liver
7	chr6:5080600-5082600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:5080600-5083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:5080600-5083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:5080800-5082000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:5080800-5083400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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