Variant report

Variant	rs811259
Chromosome Location	chr6:5007870-5007871
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	NR2F2	chr6:5007809-5008112	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5006973..5009599-chr6:5012342..5015165,2	K562	blood:
2	chr6:5002962..5005318-chr6:5007780..5009335,2	MCF-7	breast:

Variant related genes	Relation type
RPP40	TF binding region
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1108040	0.85[ASN][1000 genomes]
rs1108041	0.89[ASN][1000 genomes]
rs11967778	1.00[JPT][hapmap]
rs11967814	1.00[JPT][hapmap]
rs1627212	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17139235	1.00[JPT][hapmap]
rs1749155	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771868	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771873	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771874	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1815673	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1815674	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1815675	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002380	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2147705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764128	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764131	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764133	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764140	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764144	0.94[EUR][1000 genomes]
rs2764147	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764150	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764153	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764154	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793239	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793246	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2793252	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793253	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793254	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793256	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793257	0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793258	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793259	0.82[ASN][1000 genomes]
rs2985677	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2994695	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2994696	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4246072	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4281005	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59638108	0.88[ASN][1000 genomes]
rs62385113	0.80[ASN][1000 genomes]
rs62385115	0.80[ASN][1000 genomes]
rs62385117	0.80[ASN][1000 genomes]
rs62385118	0.80[ASN][1000 genomes]
rs62385119	0.80[ASN][1000 genomes]
rs62385121	0.88[ASN][1000 genomes]
rs62385122	0.88[ASN][1000 genomes]
rs62385123	0.81[ASN][1000 genomes]
rs707964	0.83[GIH][hapmap]
rs726743	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754334	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs877229	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9328283	0.88[ASN][1000 genomes]
rs9328284	0.81[ASN][1000 genomes]
rs9378925	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	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	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 target site	13 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs811259	FOXF2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5004600-5014000	Weak transcription	Lung	lung
2	chr6:5004800-5012200	Weak transcription	Ovary	ovary
3	chr6:5004800-5012800	Weak transcription	Aorta	Aorta
4	chr6:5004800-5013000	Weak transcription	Esophagus	oesophagus
5	chr6:5005000-5008000	Weak transcription	Spleen	Spleen
6	chr6:5005200-5008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:5005200-5008000	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:5005200-5008000	Weak transcription	Fetal Thymus	thymus
9	chr6:5005200-5012400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:5005200-5013000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:5005200-5013000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:5005200-5013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:5005200-5014200	Weak transcription	Primary T cells from cord blood	blood
14	chr6:5005200-5017000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:5005200-5025800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:5005400-5012400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:5005400-5012800	Weak transcription	HepG2	liver
18	chr6:5006800-5011400	Weak transcription	Gastric	stomach
19	chr6:5007800-5008000	Enhancers	K562	blood

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