Variant report

Variant	rs6569916
Chromosome Location	chr6:134213779-134213780
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	chr6:134211768-134214546	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:134211788-134215010	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr6:134213673-134213791	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr6:134213672-134214798	H1-hESC	embryonic stem cell:	n/a	n/a
5	SUZ12	chr6:134213542-134214999	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
ENSG00000227954	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1208276	0.89[CEU][hapmap]
rs1208277	0.89[CEU][hapmap]
rs1414669	0.86[EUR][1000 genomes]
rs149418	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572425	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162183	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162184	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162186	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162187	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162188	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327431	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2327433	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2327434	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs328455	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs328456	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896012	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932322	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693702	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7766238	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7774514	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389113	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9389114	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402546	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402547	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34122	chr6:134089019-134378252	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134209200-134215200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
2	chr6:134209400-134214000	Active TSS	Ovary	ovary
3	chr6:134210000-134214000	Active TSS	NHLF	lung
4	chr6:134211200-134214400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
5	chr6:134211800-134213800	Active TSS	A549	lung
6	chr6:134212200-134214800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:134212200-134215000	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr6:134212400-134213800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:134212400-134214400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:134212600-134214000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:134212600-134214000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:134212600-134214400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr6:134212600-134214400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
14	chr6:134212600-134214600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:134212600-134214600	Bivalent/Poised TSS	Colonic Mucosa	Colon
16	chr6:134212600-134214600	Bivalent/Poised TSS	Fetal Lung	lung
17	chr6:134212800-134214400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr6:134212800-134215400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
19	chr6:134212800-134217000	Active TSS	Right Atrium	heart
20	chr6:134213000-134214200	Active TSS	Right Ventricle	heart
21	chr6:134213000-134215400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr6:134213200-134213800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
23	chr6:134213200-134213800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:134213200-134213800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr6:134213200-134213800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
26	chr6:134213200-134213800	Bivalent/Poised TSS	Placenta	Placenta
27	chr6:134213200-134214000	Bivalent/Poised TSS	Left Ventricle	heart
28	chr6:134213200-134214600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:134213200-134215800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:134213200-134216200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:134213400-134214200	Enhancers	Hela-S3	cervix
32	chr6:134213600-134213800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr6:134213600-134213800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
34	chr6:134213600-134213800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
35	chr6:134213600-134214000	Bivalent Enhancer	Fetal Brain Female	brain
36	chr6:134213600-134214000	Enhancers	Gastric	stomach
37	chr6:134213600-134214400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:134213600-134214400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:134213600-134214600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr6:134213600-134214600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr6:134213600-134214800	Enhancers	Pancreas	Pancrea
42	chr6:134213600-134215400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
43	chr6:134213600-134216600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links