Variant report

Variant	rs8040134
Chromosome Location	chr15:49623318-49623319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49590980..49593614-chr15:49622118..49624622,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10467993	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10851475	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs10851476	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs11070685	0.86[YRI][hapmap]
rs11070687	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11630937	0.80[EUR][1000 genomes]
rs11852825	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11854667	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12437486	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438777	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs12899761	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12902497	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12903238	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12903904	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12904171	0.95[EUR][1000 genomes]
rs12909779	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12915792	0.83[YRI][hapmap]
rs12916840	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1594188	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16962440	0.83[JPT][hapmap];0.80[MEX][hapmap]
rs1816293	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1864299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1904313	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1904316	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs1981995	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2043036	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2099141	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2163095	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2163096	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2244224	0.80[YRI][hapmap]
rs2247517	0.92[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2264508	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2413935	0.85[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2413941	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2439133	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2457228	0.85[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2457229	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2663089	0.85[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs28374976	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28653543	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28687437	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2899431	0.96[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098613	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3098619	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3098621	0.96[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3105858	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3105864	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3105866	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs3907313	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4393519	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4421927	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4508377	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4774537	0.96[CEU][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4775801	0.82[YRI][hapmap]
rs4775809	0.93[ASN][1000 genomes]
rs4775810	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs481466	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs489813	0.94[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs520495	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs568726	0.85[CEU][hapmap]
rs577614	0.89[YRI][hapmap]
rs604765	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs609434	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs612803	0.96[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62009779	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs626295	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs626855	0.85[CEU][hapmap]
rs633333	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6493356	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6493357	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6493359	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6493361	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6493362	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6493366	0.83[YRI][hapmap]
rs6493367	0.83[YRI][hapmap]
rs66499252	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs672777	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs685172	0.85[CEU][hapmap]
rs694882	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7162360	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7166847	0.96[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7168201	0.95[CEU][hapmap];0.89[CHB][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7169443	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7173761	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7176697	0.80[YRI][hapmap]
rs7177959	0.80[MKK][hapmap];0.86[YRI][hapmap]
rs7179127	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7179237	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs735495	0.80[JPT][hapmap]
rs8024102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8025237	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8031480	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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];0.95[ASN][1000 genomes]
rs8034112	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs8034956	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8035266	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8039512	0.96[CEU][hapmap];0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8039920	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8040116	0.86[YRI][hapmap]
rs8041461	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8182081	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs919447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9806208	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9806362	0.80[AFR][1000 genomes]
rs9806776	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs981612	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8040134	COPS2	Cis_1M	lymphoblastoid	RTeQTL
rs8040134	SPATA5L1	cis	parietal	SCAN
rs8040134	LCMT2	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
2	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
4	chr15:49597200-49624800	Weak transcription	Fetal Kidney	kidney
5	chr15:49597400-49624200	Weak transcription	K562	blood
6	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:49607200-49623800	Weak transcription	Psoas Muscle	Psoas
8	chr15:49607600-49624400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:49612000-49624200	Weak transcription	Lung	lung
12	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
13	chr15:49612200-49639000	Weak transcription	NHEK	skin
14	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
15	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
17	chr15:49613000-49624400	Weak transcription	GM12878-XiMat	blood
18	chr15:49613000-49627600	Weak transcription	HUVEC	blood vessel
19	chr15:49613000-49628200	Weak transcription	Ovary	ovary
20	chr15:49613000-49633200	Weak transcription	Gastric	stomach
21	chr15:49613200-49625000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:49613200-49625000	Weak transcription	Hela-S3	cervix
23	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:49613600-49625400	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:49613600-49633800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:49613600-49637200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
28	chr15:49613800-49625000	Weak transcription	Fetal Brain Female	brain
29	chr15:49613800-49632600	Weak transcription	Fetal Thymus	thymus
30	chr15:49613800-49639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:49614000-49624400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:49614000-49624400	Weak transcription	NHLF	lung
33	chr15:49614200-49631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:49614200-49631600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:49614200-49631800	Weak transcription	Aorta	Aorta
36	chr15:49614200-49632000	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:49614200-49637200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:49614200-49640200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:49614200-49640200	Weak transcription	Small Intestine	intestine
40	chr15:49614400-49633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:49614400-49634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:49614800-49628800	Weak transcription	Osteobl	bone
43	chr15:49614800-49631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:49614800-49639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:49615600-49628400	Weak transcription	Adipose Nuclei	Adipose
46	chr15:49615800-49626600	Weak transcription	Fetal Stomach	stomach
47	chr15:49615800-49633600	Weak transcription	Placenta	Placenta
48	chr15:49615800-49636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:49616000-49641400	Weak transcription	Fetal Lung	lung
50	chr15:49616600-49624400	Weak transcription	H9 Cell Line	embryonic stem cell

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