Variant report

Variant	rs16901016
Chromosome Location	chr8:90852144-90852145
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90850950..90853766-chr8:90995447..90997024,2	K562	blood:
2	chr8:90835990..90838723-chr8:90850259..90852353,2	K562	blood:
3	chr8:90845301..90847765-chr8:90850348..90853325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253349	Chromatin interaction
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10094579	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096271	0.93[ASN][1000 genomes]
rs11785163	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs12155807	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675822	0.88[YRI][hapmap]
rs12680009	0.93[YRI][hapmap]
rs13260987	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs13262484	0.81[CEU][hapmap]
rs13278954	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13280951	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16900888	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2338882	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2338883	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs28405481	0.82[EUR][1000 genomes]
rs28461337	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28528187	0.99[EUR][1000 genomes]
rs28766093	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2879287	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs34525502	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34642426	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34699769	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34970073	0.83[EUR][1000 genomes]
rs35183880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39771	0.81[ASN][1000 genomes]
rs426240	0.81[ASN][1000 genomes]
rs62530862	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62530908	0.84[EUR][1000 genomes]
rs6984540	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013987	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7015630	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16901016	RIPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90847600-90860600	Weak transcription	Aorta	Aorta
2	chr8:90850000-90853000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:90850200-90852200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr8:90850200-90852800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:90850200-90853200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:90850200-90853200	Weak transcription	NHLF	lung
7	chr8:90850200-90853800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:90850200-90853800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr8:90850200-90853800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:90850200-90853800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:90850200-90853800	Weak transcription	Osteobl	bone
12	chr8:90850200-90860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:90850400-90852200	Weak transcription	HUVEC	blood vessel
14	chr8:90850400-90852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:90850400-90852600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:90850400-90853200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr8:90850400-90853200	Weak transcription	NHDF-Ad	bronchial
18	chr8:90850400-90854400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr8:90850400-90860200	Weak transcription	GM12878-XiMat	blood
20	chr8:90850800-90854600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr8:90851400-90853200	Weak transcription	A549	lung
22	chr8:90851600-90852600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr8:90851800-90852200	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links