Variant report

Variant	rs10055683
Chromosome Location	chr5:76002696-76002697
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	chr5:75997963..75999602-chr5:76001084..76003295,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10036196	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10036832	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10053089	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10056368	0.82[ASN][1000 genomes]
rs10056941	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10060848	0.85[ASN][1000 genomes]
rs10062454	0.91[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10063755	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10063791	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10063832	0.86[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10213750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10213957	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10214128	0.91[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10214133	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10214134	0.87[EUR][1000 genomes]
rs10942789	0.91[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10942790	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11950408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11951708	0.84[EUR][1000 genomes]
rs11951902	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs11952627	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs11953613	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11956898	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12054930	0.82[EUR][1000 genomes]
rs12054935	0.91[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12697858	0.91[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs13154881	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13154915	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13168057	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13175585	0.91[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13181615	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13188539	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13188565	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13188750	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1472215	0.82[CHD][hapmap]
rs2307122	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2307123	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307124	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28609562	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3797451	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3797452	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3816909	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3822547	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3822548	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4703715	0.82[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4704354	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704355	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704356	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704357	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71630933	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7712485	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7717826	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7731047	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882207	chr5:75997213-76027823	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882208	chr5:75997213-76034355	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75948000-76004600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:75977600-76003400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:75978400-76004400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:75978600-76003400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr5:75985800-76004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:75988400-76004600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:75988600-76007800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:75988800-76006600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:75988800-76011000	Weak transcription	Lung	lung
10	chr5:75989600-76010400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:75991400-76010600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:75991600-76005800	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:75993800-76004200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:75994200-76006400	Weak transcription	GM12878-XiMat	blood
15	chr5:75995800-76004000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:75997200-76010400	Weak transcription	HepG2	liver
17	chr5:75997800-76004200	Weak transcription	HMEC	breast
18	chr5:75997800-76010000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:75997800-76010800	Weak transcription	Gastric	stomach
20	chr5:75997800-76010800	Weak transcription	Pancreas	Pancrea
21	chr5:75998000-76004200	Weak transcription	Spleen	Spleen
22	chr5:75998000-76007400	Weak transcription	Fetal Stomach	stomach
23	chr5:75998200-76010000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:75998400-76010800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:75998600-76009200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:75998600-76010000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:75998600-76010600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:75998800-76004200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:75998800-76004200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:75999600-76010400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:75999800-76004000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:75999800-76004000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:75999800-76007200	Weak transcription	Stomach Mucosa	stomach
34	chr5:76000000-76004000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:76000000-76004000	Weak transcription	Primary B cells from cord blood	blood
36	chr5:76000400-76007200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:76000600-76004200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:76000600-76004400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:76001000-76003000	Enhancers	NHLF	lung
40	chr5:76001400-76004200	Weak transcription	Primary T cells from cord blood	blood
41	chr5:76001600-76007200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:76001800-76004000	Weak transcription	Placenta	Placenta
43	chr5:76001800-76004200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:76001800-76005000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:76001800-76005800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr5:76001800-76010200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:76002000-76002800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:76002000-76005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:76002000-76005600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr5:76002200-76002800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links