Variant report

Variant	rs200856
Chromosome Location	chr6:5084410-5084411
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	MAX	chr6:5084388-5084832	GM12878	blood:	n/a	chr6:5084689-5084698
2	POLR2A	chr6:5084374-5084936	HepG2	liver:	n/a	n/a
3	TCF12	chr6:5084394-5085189	ECC-1	luminal epithelium:	n/a	chr6:5084576-5084586
4	EGR1	chr6:5084392-5084966	ECC-1	luminal epithelium:	n/a	chr6:5084629-5084639 chr6:5084614-5084624 chr6:5084614-5084627 chr6:5084689-5084699 chr6:5084687-5084700
5	POLR2A	chr6:5084337-5084985	HepG2	liver:	n/a	n/a
6	SMARCB1	chr6:5084261-5086221	Hela-S3	cervix:	n/a	n/a
7	EP300	chr6:5084310-5085351	ECC-1	luminal epithelium:	n/a	chr6:5084820-5084836 chr6:5084923-5084932 chr6:5084824-5084840 chr6:5085062-5085078 chr6:5084618-5084631 chr6:5085064-5085080
8	TAF1	chr6:5084396-5085065	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:5082575-5085730	Hela-S3	cervix:	n/a	n/a
10	HEY1	chr6:5084325-5085070	HepG2	liver:	n/a	chr6:5084687-5084702
11	MAZ	chr6:5084294-5085373	K562	blood:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
12	MAX	chr6:5084396-5084960	ECC-1	luminal epithelium:	n/a	chr6:5084689-5084698
13	YY1	chr6:5084302-5085169	HepG2	liver:	n/a	chr6:5084897-5084911 chr6:5084917-5084931 chr6:5084926-5084940 chr6:5085073-5085082 chr6:5084902-5084911 chr6:5084689-5084703 chr6:5084923-5084932
14	POLR2A	chr6:5084386-5085402	K562	blood:	n/a	n/a
15	POLR2A	chr6:5084397-5084945	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:5084403-5085064	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:5084345-5085313	Hela-S3	cervix:	n/a	n/a
18	ZBTB7A	chr6:5084358-5085535	ECC-1	luminal epithelium:	n/a	chr6:5084709-5084717
19	MAX	chr6:5084076-5085263	HepG2	liver:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245

No.	Distal block	Cell Line	Cell type
1	chr6:5083037..5085353-chr6:5088863..5093171,5	MCF-7	breast:
2	chr6:5082435..5084667-chr6:5094252..5095807,2	K562	blood:
3	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];0.90[MEX][hapmap]
rs13340416	0.83[ASN][1000 genomes]
rs200852	1.00[CHD][hapmap];0.95[MEX][hapmap];0.80[ASN][1000 genomes]
rs200853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200854	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]
rs200855	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374283	0.83[ASN][1000 genomes]
rs378259	0.83[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	0.83[ASN][1000 genomes]
rs421273	0.83[ASN][1000 genomes]
rs436556	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378928	0.91[CHD][hapmap]
rs9378930	0.83[ASN][1000 genomes]
rs9378931	0.83[ASN][1000 genomes]
rs9392070	0.82[CHD][hapmap]
rs9392650	0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[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
rs200856	LYRM4	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

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	chr6:5082000-5084800	Enhancers	HMEC	breast
4	chr6:5082600-5084800	Enhancers	Placenta	Placenta
5	chr6:5083000-5084600	Enhancers	NH-A	brain
6	chr6:5083200-5084600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:5083200-5084600	Weak transcription	Gastric	stomach
8	chr6:5083400-5084600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:5083400-5084800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr6:5083800-5085000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
11	chr6:5084000-5084600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:5084000-5084800	Weak transcription	NHEK	skin
13	chr6:5084200-5084800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr6:5084200-5084800	Weak transcription	NHLF	lung
15	chr6:5084200-5085000	Active TSS	Adipose Nuclei	Adipose
16	chr6:5084200-5085000	Bivalent/Poised TSS	Fetal Stomach	stomach
17	chr6:5084200-5085200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:5084200-5086000	Active TSS	Right Ventricle	heart
19	chr6:5084200-5087400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:5084400-5084600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:5084400-5084600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:5084400-5084600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:5084400-5084600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
24	chr6:5084400-5084600	Active TSS	Primary B cells from cord blood	blood
25	chr6:5084400-5084600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
26	chr6:5084400-5084600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:5084400-5084600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:5084400-5084600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr6:5084400-5084600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
30	chr6:5084400-5084600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr6:5084400-5084600	Enhancers	Pancreas	Pancrea
32	chr6:5084400-5084600	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:5084400-5084600	Flanking Active TSS	Hela-S3	cervix
34	chr6:5084400-5084600	Flanking Active TSS	K562	blood
35	chr6:5084400-5084800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:5084400-5084800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:5084400-5084800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:5084400-5084800	Flanking Active TSS	Esophagus	oesophagus
39	chr6:5084400-5084800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr6:5084400-5085000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:5084400-5085000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:5084400-5085000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr6:5084400-5085000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:5084400-5085000	Active TSS	Brain Hippocampus Middle	brain
45	chr6:5084400-5085000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr6:5084400-5085000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
47	chr6:5084400-5085000	Bivalent Enhancer	Fetal Thymus	thymus
48	chr6:5084400-5085000	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:5084400-5085000	Active TSS	HUVEC	blood vessel
50	chr6:5084400-5085000	Active TSS	Osteobl	bone

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