Variant report

Variant	rs2687145
Chromosome Location	chr7:99318644-99318645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10211	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10227637	0.82[AMR][1000 genomes]
rs10229552	0.84[ASN][1000 genomes]
rs10238965	0.84[JPT][hapmap]
rs10242455	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10254729	0.84[JPT][hapmap]
rs10258552	0.81[ASN][1000 genomes]
rs10282706	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11772470	0.84[JPT][hapmap]
rs12334072	0.82[ASN][1000 genomes]
rs12334077	0.84[ASN][1000 genomes]
rs12360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13362853	0.83[ASN][1000 genomes]
rs1357319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403196	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419745	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs15524	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.85[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[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1851425	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1851427	0.86[ASN][1000 genomes]
rs1859690	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1879859	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][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]
rs2005548	0.80[ASN][1000 genomes]
rs2037497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090949	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140128	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177180	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2222411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2404769	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404770	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];1.00[ASN][1000 genomes]
rs2687072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2687076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687078	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687079	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687081	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687084	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687085	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687086	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]
rs2687087	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2687133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687134	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687135	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687136	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];0.91[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]
rs2687137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687139	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];1.00[ASN][1000 genomes]
rs2687140	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2740558	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2740559	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2740560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2740561	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]
rs2740562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2740563	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740565	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]
rs2741872	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2948343	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2948344	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3735453	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs3800960	0.82[JPT][hapmap]
rs45442295	0.88[ASN][1000 genomes]
rs45600842	0.88[ASN][1000 genomes]
rs45624139	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646446	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs4646447	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs4646449	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs4646450	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4646453	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs4646456	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs4646457	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4646458	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs4646461	0.98[ASN][1000 genomes]
rs4646462	0.86[ASN][1000 genomes]
rs4646465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55852703	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58649180	0.98[ASN][1000 genomes]
rs59172435	0.86[ASN][1000 genomes]
rs60298785	0.86[ASN][1000 genomes]
rs61593387	0.86[ASN][1000 genomes]
rs6465750	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6961634	0.84[JPT][hapmap]
rs72494453	0.84[ASN][1000 genomes]
rs72494454	0.86[ASN][1000 genomes]
rs72494455	0.98[ASN][1000 genomes]
rs72494456	0.86[ASN][1000 genomes]
rs73410654	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776739	0.86[EUR][1000 genomes]
rs776741	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs776742	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs776744	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs776745	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs776746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7780328	0.82[AMR][1000 genomes]
rs7808022	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs868564	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs939955	0.86[ASN][1000 genomes]
rs9769359	0.81[AMR][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	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
3	nsv888771	chr7:99294762-99355278	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv3378448	chr7:99295540-99331065	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2687145	COPS6	cis	lymphoblastoid	seeQTL
rs2687145	NINJ2	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99303200-99337200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:99306000-99339000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:99306800-99340800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:99307200-99334400	Weak transcription	Left Ventricle	heart
5	chr7:99311800-99349000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:99314800-99334400	Weak transcription	Esophagus	oesophagus
7	chr7:99315600-99331200	Weak transcription	Aorta	Aorta
8	chr7:99317000-99319200	Enhancers	HepG2	liver
9	chr7:99317000-99320800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:99317200-99318800	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr7:99317200-99319200	Enhancers	Primary T cells from cord blood	blood
12	chr7:99317400-99318800	Enhancers	Duodenum Mucosa	Duodenum
13	chr7:99317400-99318800	Enhancers	Fetal Intestine Large	intestine
14	chr7:99317400-99318800	Enhancers	Fetal Intestine Small	intestine
15	chr7:99317400-99318800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr7:99317400-99318800	Enhancers	Stomach Mucosa	stomach
17	chr7:99317400-99319200	Enhancers	Dnd41	blood
18	chr7:99317400-99320600	Enhancers	Fetal Lung	lung
19	chr7:99317600-99320600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr7:99317800-99318800	Enhancers	Adipose Nuclei	Adipose
21	chr7:99317800-99318800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr7:99318000-99318800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr7:99318000-99319400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr7:99318000-99319600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:99318000-99334600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:99318200-99320200	Weak transcription	K562	blood
27	chr7:99318200-99326000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:99318400-99318800	Enhancers	Ovary	ovary
29	chr7:99318400-99318800	Enhancers	Pancreas	Pancrea
30	chr7:99318400-99318800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr7:99318400-99319600	Enhancers	Fetal Stomach	stomach
32	chr7:99318400-99319800	Enhancers	Liver	Liver

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