Variant report

Variant	rs12440691
Chromosome Location	chr15:77146595-77146596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011083	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1011084	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10444809	0.89[ASN][1000 genomes]
rs10851889	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072612	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072616	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072618	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072619	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072620	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072625	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072626	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072628	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072631	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629727	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630402	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631082	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11631394	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632365	0.81[AMR][1000 genomes]
rs11632670	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632765	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11633869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634266	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634428	0.82[AMR][1000 genomes]
rs11635273	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637494	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852395	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855296	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855534	0.91[ASN][1000 genomes]
rs12439141	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440511	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440965	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12592686	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12898416	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904149	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904417	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905181	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906715	0.80[AMR][1000 genomes]
rs12910081	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910820	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913024	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913730	0.92[ASN][1000 genomes]
rs1443115	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1484990	0.84[ASN][1000 genomes]
rs2137311	0.92[ASN][1000 genomes]
rs2404604	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28823285	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34215663	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34998733	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35374222	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35710279	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36114653	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4312276	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886837	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55746932	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56339024	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60702982	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62029232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178250	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025991	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920712	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635380	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[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
rs12440691	SCAPER	cis	Nerve Tibial	GTEx
rs12440691	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs12440691	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12440691	SCAPER	cis	Thyroid	GTEx
rs12440691	SCAPER	cis	Esophagus Mucosa	GTEx
rs12440691	SCAPER	cis	Stomach	GTEx
rs12440691	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs12440691	SCAPER	cis	Adipose Subcutaneous	GTEx
rs12440691	SCAPER	cis	lung	GTEx
rs12440691	SCAPER	cis	Whole Blood	GTEx
rs12440691	SCAPER	cis	Artery Tibial	GTEx
rs12440691	SCAPER	cis	Esophagus Muscularis	GTEx

Chromatin state (count:82 , 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	chr15:77130600-77147400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:77131200-77155600	Weak transcription	Left Ventricle	heart
9	chr15:77131400-77148000	Weak transcription	Placenta	Placenta
10	chr15:77133200-77147600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:77139800-77155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:77139800-77158400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:77140000-77153600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:77141400-77171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:77141600-77146800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:77141800-77147400	Weak transcription	Fetal Kidney	kidney
19	chr15:77141800-77168000	Weak transcription	Spleen	Spleen
20	chr15:77142000-77148200	Weak transcription	Gastric	stomach
21	chr15:77142000-77158000	Weak transcription	Brain Angular Gyrus	brain
22	chr15:77142000-77167200	Weak transcription	Esophagus	oesophagus
23	chr15:77142000-77167800	Weak transcription	Pancreas	Pancrea
24	chr15:77142000-77175800	Weak transcription	Fetal Brain Male	brain
25	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
26	chr15:77142200-77167600	Weak transcription	Lung	lung
27	chr15:77142800-77147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:77142800-77147600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:77142800-77166400	Weak transcription	Thymus	Thymus
30	chr15:77143200-77146600	Weak transcription	Fetal Stomach	stomach
31	chr15:77143200-77149800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:77143400-77148600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:77143600-77147000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:77144000-77146600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr15:77144400-77146600	Strong transcription	Liver	Liver
36	chr15:77144400-77148000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:77144400-77149200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:77144600-77149600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:77144800-77147400	Weak transcription	HSMM	muscle
40	chr15:77144800-77179000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:77145000-77158000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:77145200-77146600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:77145200-77148400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:77145200-77148600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:77145200-77158200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:77145200-77158400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:77145400-77146600	Strong transcription	Pancreatic Islets	Pancreatic Islet
48	chr15:77145600-77146600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:77145600-77146600	Strong transcription	Aorta	Aorta
50	chr15:77145600-77146600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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