Variant report

Variant	rs12913024
Chromosome Location	chr15:77145216-77145217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1011083	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1011084	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10444809	0.89[ASN][1000 genomes]
rs10851889	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851892	0.88[AFR][1000 genomes]
rs11072612	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072616	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072618	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072619	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072620	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072625	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072626	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072628	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629727	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630402	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631082	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631394	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632365	0.87[AMR][1000 genomes]
rs11632670	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632765	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11633869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634266	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634428	0.87[AMR][1000 genomes]
rs11635273	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637494	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852395	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855296	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855534	0.91[ASN][1000 genomes]
rs12439141	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440511	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440691	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440965	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12592686	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898416	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12904149	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904417	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905181	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910081	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910820	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12913730	0.93[ASN][1000 genomes]
rs1443115	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1484990	0.85[ASN][1000 genomes]
rs2137311	0.93[ASN][1000 genomes]
rs2404600	0.88[AFR][1000 genomes]
rs2404604	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28823285	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34215663	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34998733	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35374222	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35710279	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36114653	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4312276	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886837	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55746932	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56339024	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60702982	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62029232	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178250	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8025991	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907593	0.80[AFR][1000 genomes]
rs920712	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9635380	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12913024	SCAPER	cis	Artery Tibial	GTEx
rs12913024	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs12913024	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12913024	SCAPER	cis	Whole Blood	GTEx
rs12913024	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs12913024	SCAPER	cis	Esophagus Muscularis	GTEx
rs12913024	SCAPER	cis	Esophagus Mucosa	GTEx
rs12913024	SCAPER	cis	Thyroid	GTEx
rs12913024	SCAPER	cis	Adipose Subcutaneous	GTEx
rs12913024	SCAPER	cis	lung	GTEx
rs12913024	SCAPER	cis	Muscle Skeletal	GTEx
rs12913024	SCAPER	cis	Nerve Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77111600-77174200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:77120400-77158400	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77123200-77153200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:77124400-77149600	Weak transcription	HepG2	liver
6	chr15:77125800-77175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:77126000-77145600	Weak transcription	Aorta	Aorta
8	chr15:77130600-77147400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:77131200-77155600	Weak transcription	Left Ventricle	heart
10	chr15:77131400-77148000	Weak transcription	Placenta	Placenta
11	chr15:77133200-77147600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:77139800-77145600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:77139800-77155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:77139800-77158400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:77140000-77153600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:77141200-77146400	ZNF genes & repeats	GM12878-XiMat	blood
19	chr15:77141400-77171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:77141600-77146800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:77141800-77147400	Weak transcription	Fetal Kidney	kidney
22	chr15:77141800-77168000	Weak transcription	Spleen	Spleen
23	chr15:77142000-77148200	Weak transcription	Gastric	stomach
24	chr15:77142000-77158000	Weak transcription	Brain Angular Gyrus	brain
25	chr15:77142000-77167200	Weak transcription	Esophagus	oesophagus
26	chr15:77142000-77167800	Weak transcription	Pancreas	Pancrea
27	chr15:77142000-77175800	Weak transcription	Fetal Brain Male	brain
28	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
29	chr15:77142200-77145400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:77142200-77167600	Weak transcription	Lung	lung
31	chr15:77142600-77146200	Strong transcription	Ovary	ovary
32	chr15:77142800-77147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:77142800-77147600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:77142800-77166400	Weak transcription	Thymus	Thymus
35	chr15:77143000-77145400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr15:77143000-77145800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:77143200-77145600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:77143200-77145600	Weak transcription	Fetal Intestine Small	intestine
39	chr15:77143200-77146600	Weak transcription	Fetal Stomach	stomach
40	chr15:77143200-77149800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:77143400-77145600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:77143400-77145800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr15:77143400-77146400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
44	chr15:77143400-77148600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:77143600-77147000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:77143800-77145400	ZNF genes & repeats	Fetal Lung	lung
47	chr15:77143800-77146000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr15:77144000-77145600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
49	chr15:77144000-77145800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
50	chr15:77144000-77146000	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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