Variant report

Variant	rs6855628
Chromosome Location	chr4:122072205-122072206
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	chr4:122071769..122073481-chr4:122078376..122080913,2	K562	blood:

Variant related genes	Relation type
ENSG00000050730	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10004221	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10007399	0.89[AMR][1000 genomes]
rs10015340	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10446733	0.81[EUR][1000 genomes]
rs10454795	0.81[EUR][1000 genomes]
rs10518383	0.92[GIH][hapmap];0.91[TSI][hapmap]
rs11098605	0.85[ASN][1000 genomes]
rs11947841	0.83[EUR][1000 genomes]
rs13101385	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13102428	0.83[EUR][1000 genomes]
rs13104663	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13104875	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13106137	0.81[EUR][1000 genomes]
rs13107912	0.81[EUR][1000 genomes]
rs13112923	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13115256	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116936	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13118027	0.81[EUR][1000 genomes]
rs13123960	0.83[EUR][1000 genomes]
rs13124511	0.83[EUR][1000 genomes]
rs13124522	0.83[EUR][1000 genomes]
rs13125962	0.86[ASN][1000 genomes]
rs13126929	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13128962	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13129000	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13129293	0.81[EUR][1000 genomes]
rs13129450	0.82[AMR][1000 genomes]
rs13133584	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13133740	0.86[CEU][hapmap]
rs13137539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13138203	0.92[GIH][hapmap];0.91[TSI][hapmap]
rs13143534	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13150702	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13151913	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13152159	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13152687	0.83[EUR][1000 genomes]
rs1858291	0.96[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs2136942	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2136943	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2198315	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2218959	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28513714	0.81[EUR][1000 genomes]
rs35971082	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36087391	0.83[EUR][1000 genomes]
rs3817171	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs6534254	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6811411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6812399	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812515	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6814480	0.83[EUR][1000 genomes]
rs6820363	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821331	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6833114	0.92[GIH][hapmap];0.91[TSI][hapmap]
rs6835790	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6839386	0.83[EUR][1000 genomes]
rs6846458	0.92[GIH][hapmap];0.91[TSI][hapmap]
rs6846553	0.82[CEU][hapmap]
rs6856825	0.85[EUR][1000 genomes]
rs7680038	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7684168	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs896621	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9284633	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9307490	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9992960	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9993163	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9998339	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879860	chr4:122030864-122126808	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6855628	TNIP3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122062000-122074000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr4:122067400-122073400	Enhancers	Osteobl	bone
3	chr4:122070400-122075000	Weak transcription	Fetal Lung	lung
4	chr4:122070600-122072800	Weak transcription	NHDF-Ad	bronchial
5	chr4:122071000-122073600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:122071000-122073600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:122071200-122074000	Enhancers	Primary T cells from cord blood	blood
8	chr4:122071400-122075000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:122071600-122074800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:122071600-122074800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:122071600-122075000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:122071800-122074800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr4:122072000-122073200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:122072000-122074800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:122072000-122075000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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