Variant report

Variant	rs1946650
Chromosome Location	chr15:76848463-76848464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10444858	0.88[ASN][1000 genomes]
rs11072599	0.84[CEU][hapmap]
rs11072603	0.90[ASN][1000 genomes]
rs1116535	0.96[CEU][hapmap];0.86[ASN][1000 genomes]
rs1117367	0.90[ASN][1000 genomes]
rs1125932	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12148452	0.89[ASN][1000 genomes]
rs12148877	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12437627	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438077	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438186	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438540	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440151	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441247	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12441433	0.86[ASN][1000 genomes]
rs12441550	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443137	0.91[ASN][1000 genomes]
rs12592171	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12592386	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12594541	0.87[ASN][1000 genomes]
rs12594577	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595313	0.89[ASN][1000 genomes]
rs12898430	0.90[ASN][1000 genomes]
rs12899871	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12900494	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902174	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902414	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902452	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12907805	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12908421	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911987	0.82[ASN][1000 genomes]
rs12915248	0.82[CEU][hapmap]
rs12916573	0.83[ASN][1000 genomes]
rs12917430	0.84[EUR][1000 genomes]
rs1471780	0.92[CEU][hapmap];0.86[ASN][1000 genomes]
rs1587381	0.82[CEU][hapmap]
rs1588961	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17362383	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17363713	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17364076	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17364330	0.82[CEU][hapmap]
rs17460201	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17461634	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1838048	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867197	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874944	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056544	0.87[ASN][1000 genomes]
rs2117369	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2120107	0.90[ASN][1000 genomes]
rs2120108	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164101	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2304920	0.92[CEU][hapmap];0.89[ASN][1000 genomes]
rs2404733	0.82[ASN][1000 genomes]
rs2404736	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404737	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404740	0.91[ASN][1000 genomes]
rs2404741	0.90[ASN][1000 genomes]
rs284895	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2896954	0.91[ASN][1000 genomes]
rs34060246	0.89[ASN][1000 genomes]
rs34272342	0.86[ASN][1000 genomes]
rs34287706	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34478400	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34639578	0.81[ASN][1000 genomes]
rs34707035	0.89[ASN][1000 genomes]
rs34924128	0.89[ASN][1000 genomes]
rs35077207	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35138393	0.89[ASN][1000 genomes]
rs35195096	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35395069	0.89[ASN][1000 genomes]
rs35498563	0.89[ASN][1000 genomes]
rs35566346	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36070630	0.83[ASN][1000 genomes]
rs3816266	0.93[CEU][hapmap];0.89[ASN][1000 genomes]
rs4079681	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4442773	0.92[CEU][hapmap]
rs4525456	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4641709	0.96[CEU][hapmap]
rs4886496	0.98[ASN][1000 genomes]
rs4886813	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886817	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886818	0.88[ASN][1000 genomes]
rs4886822	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886824	0.87[ASN][1000 genomes]
rs4886825	0.89[ASN][1000 genomes]
rs55676827	0.89[ASN][1000 genomes]
rs56089215	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56193230	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56216512	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56351018	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57178708	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58361452	0.89[ASN][1000 genomes]
rs58511211	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58684938	0.83[EUR][1000 genomes]
rs58973160	0.89[ASN][1000 genomes]
rs59088060	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60912217	0.86[ASN][1000 genomes]
rs6495206	0.90[ASN][1000 genomes]
rs66754747	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66986092	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67010831	0.89[ASN][1000 genomes]
rs67204011	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67232575	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67263359	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67570291	0.89[ASN][1000 genomes]
rs67888330	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67920045	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71405216	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71405222	0.84[ASN][1000 genomes]
rs71405223	0.89[ASN][1000 genomes]
rs7162455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163397	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163946	0.83[CEU][hapmap]
rs7164060	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7164813	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169394	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174953	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7179142	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72738889	0.89[ASN][1000 genomes]
rs7342603	0.93[CEU][hapmap];0.89[ASN][1000 genomes]
rs7350777	0.96[CEU][hapmap];0.89[ASN][1000 genomes]
rs7495566	0.83[ASN][1000 genomes]
rs8024476	0.93[CEU][hapmap];0.89[ASN][1000 genomes]
rs8025134	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8030411	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8036703	0.92[CEU][hapmap];0.83[ASN][1000 genomes]
rs8037005	0.83[ASN][1000 genomes]
rs8039545	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8043057	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8043474	0.93[CEU][hapmap];0.89[ASN][1000 genomes]
rs9646213	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1946650	SCAPER	cis	Nerve Tibial	GTEx
rs1946650	SCAPER	cis	Artery Tibial	GTEx
rs1946650	SCAPER	cis	lung	GTEx
rs1946650	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs1946650	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76843000-76853400	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:76843800-76850600	Weak transcription	Primary B cells from cord blood	blood
3	chr15:76845800-76851400	Weak transcription	Right Ventricle	heart
4	chr15:76846000-76862800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:76846000-76869000	Weak transcription	Left Ventricle	heart
6	chr15:76846000-76869000	Weak transcription	Pancreas	Pancrea
7	chr15:76846200-76850600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:76846200-76868800	Weak transcription	Fetal Intestine Small	intestine
9	chr15:76846600-76850800	Weak transcription	Fetal Lung	lung
10	chr15:76847000-76868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:76847200-76862400	Weak transcription	Dnd41	blood
12	chr15:76848200-76863000	Weak transcription	Primary T cells from cord blood	blood

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