Variant report

Variant	rs12595313
Chromosome Location	chr15:76978370-76978371
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	chr15:76967596..76970375-chr15:76976896..76979262,2	K562	blood:

Extended variants
information (count: 149 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10444858	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072603	0.82[ASN][1000 genomes]
rs1116535	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1117367	0.82[ASN][1000 genomes]
rs1125932	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148452	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148877	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12437627	0.89[ASN][1000 genomes]
rs12437733	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12438077	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12438186	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438540	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440151	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440835	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441247	0.84[ASN][1000 genomes]
rs12441484	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441550	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12443137	0.81[ASN][1000 genomes]
rs12591660	0.84[ASN][1000 genomes]
rs12593871	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594556	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12594577	0.84[ASN][1000 genomes]
rs12898430	0.82[ASN][1000 genomes]
rs12900494	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12902174	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902452	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903553	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904198	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12908421	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910293	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910382	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910734	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12911174	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12911902	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911987	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916869	0.82[ASN][1000 genomes]
rs1471780	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17367297	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1838048	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1867197	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1874944	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1946650	0.89[ASN][1000 genomes]
rs2120107	0.82[ASN][1000 genomes]
rs2120108	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2137307	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2304920	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404602	0.83[ASN][1000 genomes]
rs2404733	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404736	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404737	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404740	0.81[ASN][1000 genomes]
rs2896954	0.81[ASN][1000 genomes]
rs3110382	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34049670	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34060246	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181263	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34272342	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34287706	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34478400	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34639578	0.92[ASN][1000 genomes]
rs34707035	1.00[ASN][1000 genomes]
rs34924128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35077207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35138393	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35170561	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35195096	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35395069	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35557205	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35561811	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35566346	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36070630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816266	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383105	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4442773	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4525456	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4641709	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886496	0.86[ASN][1000 genomes]
rs4886503	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886813	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886817	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886818	0.81[ASN][1000 genomes]
rs4886822	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886824	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886825	1.00[ASN][1000 genomes]
rs4886829	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55676827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864032	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56193230	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56351018	0.84[ASN][1000 genomes]
rs57178708	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58361452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58511211	0.84[ASN][1000 genomes]
rs58973160	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59088060	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60658665	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60912217	0.98[ASN][1000 genomes]
rs6495206	0.82[ASN][1000 genomes]
rs66754747	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66866130	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs67010831	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67204011	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67570291	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71405216	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71405222	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71405223	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71405225	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163397	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167613	0.84[ASN][1000 genomes]
rs7169394	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174673	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174953	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72738889	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7350777	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495566	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8024476	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028294	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036703	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8037005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043474	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646213	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
11	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv904413	chr15:76923917-76995150	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv457206	chr15:76971456-77121196	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv570110	chr15:76971456-77121196	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12595313	SCAPER	cis	Artery Tibial	GTEx
rs12595313	SCAPER	cis	lung	GTEx
rs12595313	SCAPER	cis	Nerve Tibial	GTEx
rs12595313	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12595313	SCAPER	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76898400-76981000	Weak transcription	Pancreas	Pancrea
3	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76911400-76990800	Weak transcription	Placenta	Placenta
5	chr15:76936600-76991800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:76940200-76991800	Weak transcription	Left Ventricle	heart
7	chr15:76941400-76991600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:76942400-76991800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:76947400-76991600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:76947400-76991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:76954200-76992000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:76957600-76991600	Weak transcription	Liver	Liver
13	chr15:76957800-76991200	Weak transcription	Primary T cells from cord blood	blood
14	chr15:76961200-76992000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:76972400-76991400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:76972600-76991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:76972600-76991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:76973200-76991600	Weak transcription	Primary B cells from cord blood	blood
19	chr15:76973200-76991800	Weak transcription	Aorta	Aorta
20	chr15:76975000-76991800	Weak transcription	Thymus	Thymus
21	chr15:76975200-76979800	Weak transcription	Fetal Intestine Small	intestine
22	chr15:76975200-76991800	Weak transcription	Fetal Stomach	stomach
23	chr15:76976800-76991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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