Variant report

Variant	rs2627833
Chromosome Location	chr4:143172279-143172280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13109869	0.82[JPT][hapmap]
rs13120882	0.88[JPT][hapmap]
rs1343812	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs173045	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1907120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1907134	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs1907137	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1907141	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1994216	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1994217	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2130684	0.93[AMR][1000 genomes]
rs2172024	0.89[AMR][1000 genomes]
rs2245600	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2247587	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs2247659	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2322703	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs2627798	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2627804	0.95[CHB][hapmap]
rs2627813	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs2627823	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2627832	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2636630	0.91[AFR][1000 genomes]
rs2636633	0.91[AMR][1000 genomes]
rs2636645	0.84[CEU][hapmap]
rs2636674	0.81[AMR][1000 genomes]
rs2636682	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636683	0.84[CEU][hapmap]
rs2636686	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2645815	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs3102440	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3102445	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3102447	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3113522	0.81[JPT][hapmap]
rs3775692	0.81[JPT][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143058000-143181000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:143135400-143184200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:143151000-143185000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:143151200-143174000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:143153800-143181000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:143157600-143173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:143158200-143173600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:143158400-143174000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:143158600-143173800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:143159200-143181000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:143159200-143181000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:143160400-143180000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:143160600-143185000	Weak transcription	HMEC	breast
14	chr4:143160600-143186400	Weak transcription	HSMM	muscle
15	chr4:143164000-143172800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:143164400-143181000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:143164600-143176200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:143164600-143186000	Weak transcription	HSMMtube	muscle
19	chr4:143164800-143172800	Weak transcription	Primary T cells from cord blood	blood
20	chr4:143166600-143173000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:143170400-143172600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:143170400-143181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:143171000-143173200	Enhancers	NHEK	skin
24	chr4:143171000-143174000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:143171000-143185600	Weak transcription	NHDF-Ad	bronchial
26	chr4:143171000-143185800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:143171000-143186200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:143171200-143182000	Weak transcription	A549	lung
29	chr4:143171400-143172800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:143171400-143173000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:143171400-143173800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:143171400-143174000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:143171600-143182600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links