Variant report

Variant	rs17025234
Chromosome Location	chr2:40366001-40366002
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	chr2:40365962..40367921-chr2:40369317..40371065,2	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10167744	1.00[ASN][1000 genomes]
rs10167955	1.00[ASN][1000 genomes]
rs10175778	0.85[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176352	0.86[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176641	1.00[ASN][1000 genomes]
rs10183585	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs10195992	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10199306	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202413	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs10207018	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207038	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490207	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884718	0.86[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884732	0.86[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885401	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887546	0.86[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887643	0.86[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889015	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs11890878	1.00[ASN][1000 genomes]
rs11891508	1.00[ASN][1000 genomes]
rs11891921	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894296	1.00[ASN][1000 genomes]
rs11894882	1.00[ASN][1000 genomes]
rs11895025	1.00[ASN][1000 genomes]
rs11899204	1.00[ASN][1000 genomes]
rs11903986	1.00[ASN][1000 genomes]
rs12329007	1.00[ASN][1000 genomes]
rs13006841	1.00[ASN][1000 genomes]
rs13383126	1.00[ASN][1000 genomes]
rs13384452	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385280	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389962	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398048	1.00[ASN][1000 genomes]
rs13398809	1.00[ASN][1000 genomes]
rs13400484	1.00[ASN][1000 genomes]
rs13403847	0.86[EUR][1000 genomes]
rs13408531	1.00[ASN][1000 genomes]
rs13414508	1.00[ASN][1000 genomes]
rs13428581	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428681	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366424	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428574	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025157	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17025163	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17025179	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17025260	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025271	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025453	0.86[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025510	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025570	1.00[ASN][1000 genomes]
rs17025628	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs17038992	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570537	1.00[ASN][1000 genomes]
rs1896712	1.00[ASN][1000 genomes]
rs2033230	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041827	0.85[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380530	1.00[ASN][1000 genomes]
rs28660667	1.00[ASN][1000 genomes]
rs374153	1.00[ASN][1000 genomes]
rs390579	1.00[ASN][1000 genomes]
rs400673	1.00[ASN][1000 genomes]
rs405416	1.00[ASN][1000 genomes]
rs423177	1.00[ASN][1000 genomes]
rs440387	1.00[ASN][1000 genomes]
rs5554	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56092525	0.86[EUR][1000 genomes]
rs6704907	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720270	1.00[ASN][1000 genomes]
rs6728644	1.00[ASN][1000 genomes]
rs6729089	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758015	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760003	0.86[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71439287	1.00[ASN][1000 genomes]
rs73924568	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924573	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926130	1.00[ASN][1000 genomes]
rs73927124	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741320	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562916	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563045	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563290	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563445	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs7567178	1.00[ASN][1000 genomes]
rs7570501	1.00[ASN][1000 genomes]
rs7570522	1.00[ASN][1000 genomes]
rs7575693	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575802	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576587	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7583602	1.00[ASN][1000 genomes]
rs7589395	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7589951	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594419	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7594504	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs7601672	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601991	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602006	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602342	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602377	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605482	1.00[ASN][1000 genomes]
rs7607992	1.00[ASN][1000 genomes]
rs918049	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9309053	1.00[ASN][1000 genomes]
rs9653516	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873906	chr2:40341847-40385045	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873907	chr2:40349094-40381369	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1005758	chr2:40349403-40381369	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv873908	chr2:40351453-40371095	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv873909	chr2:40358526-40371095	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40354600-40366600	Weak transcription	Lung	lung
2	chr2:40355000-40366200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:40355400-40383800	Weak transcription	Small Intestine	intestine
4	chr2:40355800-40370000	Weak transcription	Fetal Brain Male	brain
5	chr2:40356000-40367400	Weak transcription	Fetal Brain Female	brain
6	chr2:40356800-40375000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:40357600-40374000	Weak transcription	HSMMtube	muscle
8	chr2:40357800-40366200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:40357800-40366200	Weak transcription	Fetal Stomach	stomach
10	chr2:40357800-40366600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:40358200-40392200	Weak transcription	NHLF	lung
14	chr2:40358800-40369200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:40358800-40389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:40359000-40387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:40360200-40366200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:40360400-40366800	Weak transcription	Ovary	ovary
19	chr2:40361000-40375000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:40361800-40369200	Strong transcription	Dnd41	blood
21	chr2:40362400-40366400	Strong transcription	Left Ventricle	heart
22	chr2:40363800-40369200	Strong transcription	HSMM	muscle
23	chr2:40364000-40366800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr2:40364200-40367400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:40364200-40377400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:40364400-40383800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:40364600-40375000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:40364600-40387000	Weak transcription	Placenta	Placenta
29	chr2:40364800-40369200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr2:40364800-40380400	Weak transcription	Fetal Intestine Small	intestine
31	chr2:40365200-40369200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:40365200-40372800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:40365400-40366600	Strong transcription	Right Ventricle	heart
35	chr2:40365400-40366800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:40365600-40366600	Strong transcription	Brain Germinal Matrix	brain
37	chr2:40365600-40366800	Strong transcription	Aorta	Aorta
38	chr2:40365600-40367000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:40365600-40367000	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:40365600-40368800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:40366000-40368400	Genic enhancers	Fetal Heart	heart
42	chr2:40366000-40368600	Strong transcription	Osteobl	bone

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