Variant report

Variant	rs10519225
Chromosome Location	chr15:49720778-49720779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10519224	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851478	1.00[YRI][hapmap]
rs10851479	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11070695	0.83[ASN][1000 genomes]
rs11070699	0.82[JPT][hapmap]
rs11070706	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs11852293	1.00[LWK][hapmap]
rs11853248	0.88[ASN][1000 genomes]
rs11853969	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11854039	1.00[AFR][1000 genomes]
rs11854557	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11854671	0.87[ASN][1000 genomes]
rs11855798	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11858411	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12050614	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12148764	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs12232355	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12591300	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591317	0.80[ASN][1000 genomes]
rs12592508	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12593151	0.90[ASN][1000 genomes]
rs12595692	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12901353	1.00[AFR][1000 genomes]
rs12901929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902096	0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902271	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12902960	0.84[ASN][1000 genomes]
rs12905203	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905477	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12906972	0.87[ASN][1000 genomes]
rs12907661	0.81[ASN][1000 genomes]
rs12907918	0.86[ASN][1000 genomes]
rs12907944	0.87[ASN][1000 genomes]
rs12908624	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12908635	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12912703	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12916839	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395901	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1395903	0.87[ASN][1000 genomes]
rs17402115	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17478694	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478785	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479589	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1874616	0.82[JPT][hapmap]
rs1911612	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1961393	1.00[AFR][1000 genomes]
rs1976551	0.81[ASN][1000 genomes]
rs2202714	0.82[JPT][hapmap]
rs2413956	0.87[ASN][1000 genomes]
rs2899434	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34002493	0.90[ASN][1000 genomes]
rs34146550	0.81[ASN][1000 genomes]
rs34246470	0.87[ASN][1000 genomes]
rs34414487	0.87[ASN][1000 genomes]
rs34562714	1.00[AFR][1000 genomes]
rs34694913	0.87[ASN][1000 genomes]
rs35698479	0.85[ASN][1000 genomes]
rs36023246	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36100631	1.00[AFR][1000 genomes]
rs4389093	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4436732	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4480740	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs4547278	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4774538	1.00[AFR][1000 genomes]
rs4775806	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs4775816	0.87[ASN][1000 genomes]
rs55904469	0.87[ASN][1000 genomes]
rs55979115	1.00[AFR][1000 genomes]
rs62009834	1.00[AFR][1000 genomes]
rs62009977	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs62021589	0.86[ASN][1000 genomes]
rs62022665	0.86[ASN][1000 genomes]
rs62022667	0.87[ASN][1000 genomes]
rs6493372	0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7162741	0.86[ASN][1000 genomes]
rs7172906	0.85[ASN][1000 genomes]
rs7174135	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7180168	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7497335	0.92[AFR][1000 genomes]
rs753857	0.82[JPT][hapmap]
rs8029687	0.82[AFR][1000 genomes]
rs925104	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs9920722	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][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	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
2	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
rs10519225	SPATA5L1	cis	parietal	SCAN
rs10519225	LCMT2	cis	parietal	SCAN
rs10519225	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49714000-49720800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr15:49714000-49721000	Active TSS	Colon Smooth Muscle	Colon
3	chr15:49714000-49722600	Active TSS	Stomach Smooth Muscle	stomach
4	chr15:49714200-49721000	Active TSS	Rectal Smooth Muscle	rectum
5	chr15:49714200-49721000	Active TSS	Right Atrium	heart
6	chr15:49714200-49721400	Active TSS	Adipose Nuclei	Adipose
7	chr15:49715400-49721600	Active TSS	NHLF	lung
8	chr15:49716200-49732200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:49716800-49720800	Weak transcription	Hela-S3	cervix
11	chr15:49716800-49722000	Weak transcription	Colonic Mucosa	Colon
12	chr15:49717000-49721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:49717600-49721200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:49718000-49727800	Weak transcription	HSMMtube	muscle
15	chr15:49718000-49731200	Weak transcription	Left Ventricle	heart
16	chr15:49719400-49731200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:49719600-49722600	Transcr. at gene 5' and 3'	Osteobl	bone
18	chr15:49720000-49720800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr15:49720200-49720800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:49720200-49721000	Active TSS	Right Ventricle	heart
21	chr15:49720400-49720800	Enhancers	Ovary	ovary
22	chr15:49720400-49721200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:49720400-49721200	Flanking Active TSS	Fetal Lung	lung
24	chr15:49720600-49720800	Enhancers	Pancreas	Pancrea
25	chr15:49720600-49720800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr15:49720600-49721000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:49720600-49721200	Enhancers	Psoas Muscle	Psoas
28	chr15:49720600-49721400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr15:49720600-49721600	Enhancers	Liver	Liver
30	chr15:49720600-49722800	Enhancers	Fetal Stomach	stomach
31	chr15:49720600-49723200	Enhancers	Fetal Heart	heart

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