Variant report

Variant	rs3127572
Chromosome Location	chr6:160682218-160682219
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	KAP1	chr6:160681697-160682260	HEK293	kidney:	n/a	chr6:160682110-160682118
2	SMC3	chr6:160681895-160682236	Hela-S3	cervix:	n/a	n/a
3	USF2	chr6:160681726-160682285	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr6:160681996-160682417	Hela-S3	cervix:	n/a	n/a
5	EP300	chr6:160682009-160682428	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr6:160681764-160682498	Hela-S3	cervix:	n/a	n/a
7	MAX	chr6:160681791-160682287	Hela-S3	cervix:	n/a	n/a
8	NFYA	chr6:160681787-160682257	Hela-S3	cervix:	n/a	chr6:160681922-160681936 chr6:160681922-160681937 chr6:160681922-160681937
9	MXI1	chr6:160681799-160682247	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr6:160681978-160682327	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr6:160681917-160682313	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SLC22A2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2279463	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs3119309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3119310	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs3119311	1.00[CEU][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs3127573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3127578	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs3798156	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7756836	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757336	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160676400-160683200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:160676600-160683000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:160679000-160683200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:160679600-160682600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:160680000-160685800	Enhancers	Fetal Intestine Large	intestine
6	chr6:160680200-160686000	Enhancers	Fetal Intestine Small	intestine
7	chr6:160680600-160682400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:160680600-160682800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:160681200-160683200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:160681200-160683400	Enhancers	Hela-S3	cervix
11	chr6:160681400-160682800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:160681400-160682800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:160681400-160683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:160681800-160682800	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:160681800-160683000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:160681800-160683600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:160681800-160684000	Enhancers	A549	lung
18	chr6:160682000-160683000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:160682000-160686800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:160682200-160682600	Weak transcription	Placenta	Placenta
21	chr6:160682200-160682600	Weak transcription	Pancreas	Pancrea
22	chr6:160682200-160683200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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