Variant report

Variant	rs4460596
Chromosome Location	chr1:175986303-175986304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10429845	0.83[AMR][1000 genomes]
rs10436864	0.85[EUR][1000 genomes]
rs10494499	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10798427	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs10798428	0.92[EUR][1000 genomes]
rs10798430	1.00[CHB][hapmap]
rs10798435	1.00[CHB][hapmap]
rs10913150	0.91[CEU][hapmap]
rs11576862	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11579181	1.00[JPT][hapmap]
rs11580753	0.87[ASN][1000 genomes]
rs11583071	0.87[ASN][1000 genomes]
rs11584481	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11587254	1.00[JPT][hapmap]
rs11587785	1.00[JPT][hapmap]
rs11588480	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11590045	0.87[ASN][1000 genomes]
rs12038027	0.90[EUR][1000 genomes]
rs12404181	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357337	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1357338	1.00[CHB][hapmap]
rs17351808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17351933	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17354252	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2481627	0.91[CEU][hapmap]
rs2481632	1.00[CHB][hapmap]
rs2481635	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2481640	1.00[CHB][hapmap]
rs2481647	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2481648	1.00[CHB][hapmap]
rs2481651	0.90[EUR][1000 genomes]
rs2481657	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2502821	1.00[CHB][hapmap]
rs2502822	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2502826	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2502827	1.00[CHB][hapmap]
rs2502828	1.00[CHB][hapmap]
rs2502832	0.91[CEU][hapmap]
rs2502836	0.91[CEU][hapmap]
rs2502837	1.00[CHB][hapmap]
rs2502841	0.91[CEU][hapmap]
rs2502842	0.91[CEU][hapmap]
rs2774925	1.00[CHB][hapmap]
rs2861630	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129061	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs4233165	1.00[CHB][hapmap]
rs4307526	0.94[EUR][1000 genomes]
rs4314844	0.94[EUR][1000 genomes]
rs4344283	1.00[CHB][hapmap]
rs4347169	1.00[CHB][hapmap]
rs4379645	1.00[CHB][hapmap]
rs4534339	1.00[CHB][hapmap]
rs4601543	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs533299	1.00[CHB][hapmap]
rs537407	1.00[CHB][hapmap]
rs553852	0.91[CEU][hapmap]
rs56051510	0.87[ASN][1000 genomes]
rs56198111	0.87[ASN][1000 genomes]
rs56949697	0.87[ASN][1000 genomes]
rs580978	0.91[CEU][hapmap]
rs598855	1.00[CHB][hapmap]
rs60719126	0.87[ASN][1000 genomes]
rs60964243	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61186664	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs613965	1.00[CHB][hapmap]
rs61820953	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61820960	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61820965	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61820968	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61820999	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61821007	0.87[ASN][1000 genomes]
rs61821009	0.87[ASN][1000 genomes]
rs61822767	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425368	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs6425369	1.00[CHB][hapmap]
rs6425372	1.00[CHB][hapmap]
rs6425374	1.00[CHB][hapmap]
rs646754	1.00[CHB][hapmap]
rs6674353	1.00[CHB][hapmap]
rs6680309	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704250	1.00[CHB][hapmap]
rs6704509	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs704827	0.91[CEU][hapmap]
rs704828	1.00[CHB][hapmap]
rs704833	1.00[CHB][hapmap]
rs74127150	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74127154	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7517351	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7523048	1.00[CHB][hapmap]
rs7524972	0.90[EUR][1000 genomes]
rs7525112	1.00[CHB][hapmap]
rs7532122	1.00[CHB][hapmap]
rs7537435	0.87[EUR][1000 genomes]
rs7541563	1.00[CHB][hapmap]
rs7545043	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs7545639	0.94[EUR][1000 genomes]
rs7552181	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7554913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791744	0.91[CEU][hapmap]
rs791748	1.00[CHB][hapmap]
rs791801	0.83[CEU][hapmap]
rs9783047	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs998631	1.00[CHB][hapmap]

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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175946000-175996000	Weak transcription	HMEC	breast
2	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
3	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
6	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:175974000-176003000	Weak transcription	NH-A	brain
8	chr1:175974400-175988200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:175974600-175988800	Weak transcription	Pancreas	Pancrea
10	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:175975400-176003400	Weak transcription	NHLF	lung
12	chr1:175975600-175988400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:175975800-175988800	Weak transcription	Ovary	ovary
14	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
15	chr1:175976400-175996000	Weak transcription	HUVEC	blood vessel
16	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:175977600-175988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:175978200-176001000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
22	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
23	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
24	chr1:175978400-175986800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:175978400-175987800	Weak transcription	Fetal Stomach	stomach
26	chr1:175978400-175988000	Weak transcription	Thymus	Thymus
27	chr1:175978400-175988600	Weak transcription	Esophagus	oesophagus
28	chr1:175978400-175989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:175978400-175996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:175978400-175996600	Weak transcription	Left Ventricle	heart
31	chr1:175978400-176001600	Weak transcription	Fetal Lung	lung
32	chr1:175978400-176003000	Weak transcription	HSMM	muscle
33	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
34	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
36	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:175978800-175988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:175978800-176003000	Weak transcription	A549	lung
43	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
44	chr1:175979400-175994800	Weak transcription	Placenta	Placenta
45	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:175979400-176012200	Weak transcription	HepG2	liver
47	chr1:175979600-175991600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:175979600-176001000	Weak transcription	NHEK	skin
49	chr1:175979600-176010600	Weak transcription	Right Ventricle	heart
50	chr1:175979600-176012000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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