Variant report

Variant	rs200852
Chromosome Location	chr6:5081745-5081746
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	chr6:5081501-5081755	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:5081363-5081767	HepG2	liver:	n/a	n/a
3	HEY1	chr6:5080827-5081791	HepG2	liver:	n/a	n/a
4	CHD2	chr6:5081599-5081749	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:5080171..5082939-chr6:5089292..5092079,2	MCF-7	breast:
2	chr6:5072255..5076149-chr6:5080723..5083422,4	K562	blood:
3	chr6:5079080..5082683-chr6:5086665..5090602,4	K562	blood:
4	chr6:5081137..5084088-chr6:5116635..5118182,2	MCF-7	breast:

Variant related genes	Relation type
PPP1R3G	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1265347	0.82[ASN][1000 genomes]
rs1265351	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]
rs13340416	0.96[ASN][1000 genomes]
rs200853	1.00[CHD][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200854	1.00[CHD][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs200855	0.80[ASN][1000 genomes]
rs200856	1.00[CHD][hapmap];0.95[MEX][hapmap];0.80[ASN][1000 genomes]
rs374283	0.96[ASN][1000 genomes]
rs376210	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs378259	0.96[ASN][1000 genomes]
rs379169	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs397654	0.84[ASN][1000 genomes]
rs398302	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421273	0.96[ASN][1000 genomes]
rs425133	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs436556	0.82[ASN][1000 genomes]
rs441144	0.82[ASN][1000 genomes]
rs449288	0.82[ASN][1000 genomes]
rs450634	0.82[ASN][1000 genomes]
rs7752352	0.82[ASN][1000 genomes]
rs9378928	0.91[CHD][hapmap]
rs9378930	0.96[ASN][1000 genomes]
rs9378931	0.96[ASN][1000 genomes]
rs9378932	0.80[ASN][1000 genomes]
rs9378933	0.82[ASN][1000 genomes]
rs9392070	0.82[CHD][hapmap]
rs9392071	0.82[ASN][1000 genomes]
rs9392649	0.81[ASN][1000 genomes]
rs9392650	0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs9392651	0.82[ASN][1000 genomes]
rs9392653	0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs9405254	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs9405255	0.83[ASN][1000 genomes]
rs9405256	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
rs200852	LYRM4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5071800-5082400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5075400-5082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:5077600-5082800	Weak transcription	Spleen	Spleen
4	chr6:5080000-5084800	Enhancers	NHDF-Ad	bronchial
5	chr6:5080400-5085400	Flanking Active TSS	HepG2	liver
6	chr6:5080600-5082600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:5080600-5083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:5080600-5083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:5080800-5082000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:5080800-5083400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:5081000-5084400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:5081400-5082000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:5081600-5081800	Enhancers	Right Ventricle	heart
14	chr6:5081600-5082400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:5081600-5082600	Enhancers	NH-A	brain
16	chr6:5081600-5084000	Enhancers	NHEK	skin

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