Variant report

Variant	rs777433
Chromosome Location	chr2:128368235-128368236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128367073..128368593-chr2:128390549..128393243,2	K562	blood:
2	chr2:128368208..128370995-chr2:128394997..128397698,2	K562	blood:

Variant related genes	Relation type
ENSG00000169994	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10928774	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10928775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11675513	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11684148	0.92[ASN][1000 genomes]
rs11691981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12052293	1.00[ASN][1000 genomes]
rs12052654	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12053039	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12053248	0.96[ASN][1000 genomes]
rs12999486	0.82[JPT][hapmap]
rs13004906	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13006453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13015157	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13025791	0.92[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs13025959	0.92[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs13034190	0.92[ASN][1000 genomes]
rs17261964	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2252610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253005	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255161	0.86[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2264726	0.85[ASN][1000 genomes]
rs2264727	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36108975	1.00[ASN][1000 genomes]
rs4662585	1.00[JPT][hapmap]
rs4662748	1.00[ASN][1000 genomes]
rs705092	0.99[ASN][1000 genomes]
rs777432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930139	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015051	chr2:128295320-128372079	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1011937	chr2:128295320-128405921	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1008294	chr2:128295320-128420654	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1007207	chr2:128295320-128429775	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003004	chr2:128295320-128474326	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv999302	chr2:128299079-128372079	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1008457	chr2:128299079-128405921	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1009514	chr2:128299079-128420654	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1006421	chr2:128299079-128473079	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv1004877	chr2:128299079-128479640	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1001624	chr2:128306660-128420654	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv875016	chr2:128330458-128401091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv875017	chr2:128330458-128445585	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv875018	chr2:128330458-128465547	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv518085	chr2:128334413-128404860	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv583037	chr2:128334470-128401091	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv875019	chr2:128340855-128408170	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv875020	chr2:128340855-128445585	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv875021	chr2:128340855-128465547	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
21	nsv470482	chr2:128350808-128465547	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs777433	SFT2D3	cis	parietal	SCAN
rs777433	GPR17	cis	Artery Aorta	GTEx
rs777433	GPR17	cis	cerebellum	SCAN
rs777433	GPR17	cis	lung	GTEx
rs777433	LIMS2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128328000-128370200	Weak transcription	Small Intestine	intestine
2	chr2:128334400-128376400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:128358800-128369000	Strong transcription	Fetal Intestine Large	intestine
4	chr2:128359000-128376000	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr2:128359200-128395200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:128360000-128375000	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:128364600-128370400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:128364800-128373200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:128365200-128368800	Strong transcription	Colonic Mucosa	Colon
10	chr2:128367000-128369400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:128367200-128369800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:128367400-128368400	Weak transcription	Placenta	Placenta
13	chr2:128367600-128370600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr2:128367800-128369200	Genic enhancers	Dnd41	blood
15	chr2:128368200-128369000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:128368200-128369400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin

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