Variant report

Variant	rs2740565
Chromosome Location	chr7:99293475-99293476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227637	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10229552	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10238965	0.84[JPT][hapmap]
rs10242455	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs10254729	0.84[JPT][hapmap]
rs10258552	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10282706	0.89[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11772470	0.84[JPT][hapmap]
rs12333599	0.84[ASN][1000 genomes]
rs12334072	0.87[ASN][1000 genomes]
rs12334077	0.88[ASN][1000 genomes]
rs12360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13362853	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1357319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1403196	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1419745	0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs15524	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17161774	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs17161780	0.80[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs17161783	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs1818797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851427	0.86[ASN][1000 genomes]
rs1859690	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1879859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037497	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2090949	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140128	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404769	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687072	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2687076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687077	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687081	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2687134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2687135	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687137	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687140	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687141	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687143	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2687145	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740558	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740559	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740560	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740562	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2740563	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2741872	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2948343	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2948344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3735453	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3800960	0.82[JPT][hapmap]
rs3823812	0.83[ASN][1000 genomes]
rs45442295	0.84[ASN][1000 genomes]
rs45600842	0.84[ASN][1000 genomes]
rs45624139	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646446	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4646447	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4646449	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4646450	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646453	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4646456	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs4646457	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs4646458	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap]
rs4646461	0.93[ASN][1000 genomes]
rs4646462	0.83[ASN][1000 genomes]
rs4646465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55852703	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58024720	0.82[ASN][1000 genomes]
rs58649180	0.93[ASN][1000 genomes]
rs59172435	0.83[ASN][1000 genomes]
rs60298785	0.83[ASN][1000 genomes]
rs61593387	0.83[ASN][1000 genomes]
rs6465750	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6961634	0.84[JPT][hapmap]
rs72494453	0.88[ASN][1000 genomes]
rs72494454	0.86[ASN][1000 genomes]
rs72494455	0.93[ASN][1000 genomes]
rs72494456	0.83[ASN][1000 genomes]
rs73410654	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs776739	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs776741	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs776742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776746	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs7780328	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7798931	0.80[ASN][1000 genomes]
rs7808022	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs868564	0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap]
rs939955	0.83[ASN][1000 genomes]
rs9769359	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482532	chr7:99205906-99363886	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv970911	chr7:99275492-99333590	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2740565	NINJ2	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99277000-99295800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:99290600-99293600	Enhancers	Fetal Intestine Small	intestine
3	chr7:99291400-99297600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:99291400-99297600	Weak transcription	Esophagus	oesophagus
5	chr7:99291400-99298800	Weak transcription	Aorta	Aorta
6	chr7:99291400-99306600	Weak transcription	Left Ventricle	heart
7	chr7:99291600-99294600	Weak transcription	Fetal Thymus	thymus
8	chr7:99291600-99295600	Weak transcription	Pancreas	Pancrea
9	chr7:99292200-99294600	Enhancers	K562	blood
10	chr7:99292200-99296200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:99292200-99296200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:99292200-99297000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:99292400-99295800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:99292400-99295800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:99292400-99295800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:99292400-99295800	Weak transcription	Stomach Mucosa	stomach
17	chr7:99292400-99296000	Weak transcription	A549	lung
18	chr7:99292400-99296400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:99292400-99298600	Enhancers	HepG2	liver
20	chr7:99292800-99294400	Enhancers	Liver	Liver
21	chr7:99293000-99293600	Enhancers	Gastric	stomach
22	chr7:99293200-99295600	Weak transcription	Fetal Intestine Large	intestine
23	chr7:99293400-99293800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links