Variant report

Variant	rs200854
Chromosome Location	chr6:5083872-5083873
allele	A/G
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	chr6:5083743-5083926	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:5082078-5083881	HepG2	liver:	n/a	n/a
3	HEY1	chr6:5081823-5084134	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:5081927-5084347	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:5083523-5083948	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:5082575-5085730	Hela-S3	cervix:	n/a	n/a
7	TFAP2C	chr6:5082351-5083999	Hela-S3	cervix:	n/a	chr6:5083050-5083065
8	POLR2A	chr6:5083675-5084005	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:5083037..5085353-chr6:5088863..5093171,5	MCF-7	breast:
2	chr6:5077831..5080462-chr6:5082551..5084098,2	K562	blood:
3	chr6:5082435..5084667-chr6:5094252..5095807,2	K562	blood:
4	chr6:5081137..5084088-chr6:5116635..5118182,2	MCF-7	breast:
5	chr6:5082094..5085573-chr6:5086074..5088451,3	K562	blood:

Variant related genes	Relation type
PPP1R3G	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1265351	0.91[CHD][hapmap];0.85[MEX][hapmap]
rs13340416	0.84[ASN][1000 genomes]
rs200852	1.00[CHD][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs200853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200855	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200856	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs374283	0.84[ASN][1000 genomes]
rs378259	0.84[ASN][1000 genomes]
rs397654	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs398302	0.84[ASN][1000 genomes]
rs421273	0.84[ASN][1000 genomes]
rs436556	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378928	0.91[CHD][hapmap]
rs9378930	0.84[ASN][1000 genomes]
rs9378931	0.84[ASN][1000 genomes]
rs9392070	0.82[CHD][hapmap]
rs9392650	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs9392653	0.91[CHD][hapmap]
rs9405254	1.00[CHD][hapmap]

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	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	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
8	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
9	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
10	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
11	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
rs200854	LYRM4	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5080000-5084800	Enhancers	NHDF-Ad	bronchial
2	chr6:5080400-5085400	Flanking Active TSS	HepG2	liver
3	chr6:5081000-5084400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:5081600-5084000	Enhancers	NHEK	skin
5	chr6:5081800-5084200	Weak transcription	Right Ventricle	heart
6	chr6:5081800-5084200	Enhancers	NHLF	lung
7	chr6:5082000-5084000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:5082000-5084400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:5082000-5084400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:5082000-5084400	Enhancers	A549	lung
11	chr6:5082000-5084800	Enhancers	HMEC	breast
12	chr6:5082200-5084400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:5082400-5084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:5082400-5084200	Enhancers	HSMM	muscle
15	chr6:5082400-5084400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr6:5082600-5084400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
17	chr6:5082600-5084800	Enhancers	Placenta	Placenta
18	chr6:5082800-5084200	Enhancers	Spleen	Spleen
19	chr6:5083000-5084400	Enhancers	K562	blood
20	chr6:5083000-5084600	Enhancers	NH-A	brain
21	chr6:5083200-5084200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:5083200-5084400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:5083200-5084400	Weak transcription	Pancreas	Pancrea
24	chr6:5083200-5084600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:5083200-5084600	Weak transcription	Gastric	stomach
26	chr6:5083400-5084000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:5083400-5084200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:5083400-5084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:5083400-5084400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:5083400-5084400	Weak transcription	Esophagus	oesophagus
31	chr6:5083400-5084400	Weak transcription	Osteobl	bone
32	chr6:5083400-5084600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:5083400-5084800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr6:5083800-5084400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:5083800-5084400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:5083800-5084400	Enhancers	Hela-S3	cervix
37	chr6:5083800-5085000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links