Variant report

Variant	rs12913730
Chromosome Location	chr15:77145669-77145670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10444809	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072619	0.85[ASN][1000 genomes]
rs11072620	0.85[ASN][1000 genomes]
rs11072625	0.86[ASN][1000 genomes]
rs11072626	0.83[ASN][1000 genomes]
rs11072628	0.91[ASN][1000 genomes]
rs11072631	0.92[ASN][1000 genomes]
rs11631082	0.85[ASN][1000 genomes]
rs11633869	0.92[ASN][1000 genomes]
rs11634266	0.86[ASN][1000 genomes]
rs11637494	0.90[ASN][1000 genomes]
rs11852395	0.86[ASN][1000 genomes]
rs11855296	0.90[ASN][1000 genomes]
rs11855534	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439141	0.86[ASN][1000 genomes]
rs12440691	0.92[ASN][1000 genomes]
rs12592686	0.90[ASN][1000 genomes]
rs12898416	0.85[ASN][1000 genomes]
rs12904149	0.83[ASN][1000 genomes]
rs12905181	0.85[ASN][1000 genomes]
rs12913024	0.93[ASN][1000 genomes]
rs1443115	0.85[ASN][1000 genomes]
rs1484990	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2137311	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823285	0.86[ASN][1000 genomes]
rs34215663	0.88[ASN][1000 genomes]
rs34998733	0.87[ASN][1000 genomes]
rs35374222	0.88[ASN][1000 genomes]
rs35710279	0.85[ASN][1000 genomes]
rs36114653	0.81[ASN][1000 genomes]
rs4312276	0.88[ASN][1000 genomes]
rs4886837	0.90[ASN][1000 genomes]
rs55746932	0.88[ASN][1000 genomes]
rs60702982	0.84[ASN][1000 genomes]
rs7178250	0.86[ASN][1000 genomes]
rs8025991	0.90[ASN][1000 genomes]
rs920712	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12913730	SCAPER	cis	Thyroid	GTEx
rs12913730	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12913730	SCAPER	cis	Artery Tibial	GTEx
rs12913730	SCAPER	cis	Adipose Subcutaneous	GTEx
rs12913730	SCAPER	cis	lung	GTEx
rs12913730	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs12913730	ISL2	cis	Whole Blood	GTEx
rs12913730	SCAPER	cis	Whole Blood	GTEx
rs12913730	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:81 , 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	chr15:77141200-77146400	ZNF genes & repeats	GM12878-XiMat	blood
17	chr15:77141400-77171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:77141600-77146800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:77141800-77147400	Weak transcription	Fetal Kidney	kidney
20	chr15:77141800-77168000	Weak transcription	Spleen	Spleen
21	chr15:77142000-77148200	Weak transcription	Gastric	stomach
22	chr15:77142000-77158000	Weak transcription	Brain Angular Gyrus	brain
23	chr15:77142000-77167200	Weak transcription	Esophagus	oesophagus
24	chr15:77142000-77167800	Weak transcription	Pancreas	Pancrea
25	chr15:77142000-77175800	Weak transcription	Fetal Brain Male	brain
26	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
27	chr15:77142200-77167600	Weak transcription	Lung	lung
28	chr15:77142600-77146200	Strong transcription	Ovary	ovary
29	chr15:77142800-77147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:77142800-77147600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:77142800-77166400	Weak transcription	Thymus	Thymus
32	chr15:77143000-77145800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:77143200-77146600	Weak transcription	Fetal Stomach	stomach
34	chr15:77143200-77149800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:77143400-77145800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:77143400-77146400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
37	chr15:77143400-77148600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:77143600-77147000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:77143800-77146000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr15:77144000-77145800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr15:77144000-77146000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr15:77144000-77146400	ZNF genes & repeats	Dnd41	blood
43	chr15:77144000-77146600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr15:77144200-77146000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
45	chr15:77144400-77146600	Strong transcription	Liver	Liver
46	chr15:77144400-77148000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:77144400-77149200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:77144600-77146400	ZNF genes & repeats	Fetal Brain Female	brain
49	chr15:77144600-77149600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:77144800-77146200	Strong transcription	Brain Hippocampus Middle	brain

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