Variant report

Variant	rs17025453
Chromosome Location	chr2:40406414-40406415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10167744	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167955	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175778	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176352	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176641	1.00[ASN][1000 genomes]
rs10183585	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199306	0.93[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202413	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs10207018	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207038	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490207	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884718	1.00[CEU][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884732	1.00[CEU][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885401	0.93[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887546	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887643	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889015	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890878	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891508	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891921	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894296	1.00[ASN][1000 genomes]
rs11894882	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895025	0.85[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899204	1.00[ASN][1000 genomes]
rs11903986	1.00[ASN][1000 genomes]
rs12329007	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006841	1.00[ASN][1000 genomes]
rs13383126	1.00[ASN][1000 genomes]
rs13384452	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385280	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389962	0.88[AMR][1000 genomes];0.97[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	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13408531	0.81[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414508	1.00[ASN][1000 genomes]
rs13428581	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428681	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366424	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428574	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025157	0.90[CEU][hapmap]
rs17025163	0.86[CEU][hapmap]
rs17025179	0.86[CEU][hapmap]
rs17025234	0.86[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025260	0.86[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025271	0.85[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025510	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025570	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025628	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17038992	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs17570537	0.87[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896712	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033230	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041827	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380530	1.00[ASN][1000 genomes]
rs28660667	0.80[EUR][1000 genomes];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	0.85[CEU][hapmap]
rs56092525	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704907	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs6720270	1.00[ASN][1000 genomes]
rs6728644	1.00[ASN][1000 genomes]
rs6729089	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758015	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760003	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71439287	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924568	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924573	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926129	0.91[EUR][1000 genomes]
rs73926130	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73927124	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741320	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562916	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563045	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563290	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563445	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567178	1.00[ASN][1000 genomes]
rs7570501	1.00[ASN][1000 genomes]
rs7570522	1.00[ASN][1000 genomes]
rs7575693	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575802	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583602	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589951	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594419	0.86[CEU][hapmap]
rs7601672	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7601991	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602006	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602342	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602377	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605482	1.00[ASN][1000 genomes]
rs7607992	0.81[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918049	0.85[CEU][hapmap]
rs9309053	0.81[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653516	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
2	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
3	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
4	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:40400600-40426800	Weak transcription	Osteobl	bone
6	chr2:40402200-40407400	Enhancers	Fetal Heart	heart
7	chr2:40404400-40406600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:40404800-40407200	Enhancers	Fetal Thymus	thymus
9	chr2:40405200-40407200	Enhancers	HSMMtube	muscle
10	chr2:40405400-40407000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:40405400-40407200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:40405400-40430000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:40405600-40407600	Enhancers	Dnd41	blood
14	chr2:40405600-40409200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:40405600-40409400	Weak transcription	Aorta	Aorta
16	chr2:40405600-40410600	Weak transcription	Left Ventricle	heart
17	chr2:40405600-40421800	Weak transcription	Right Ventricle	heart
18	chr2:40405800-40407200	Enhancers	HSMM	muscle
19	chr2:40406200-40406600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:40406200-40407200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:40406200-40407200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:40406400-40406600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:40406400-40406600	Enhancers	Thymus	Thymus
24	chr2:40406400-40416600	Weak transcription	Fetal Muscle Leg	muscle

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