Variant report

Variant	rs56339024
Chromosome Location	chr15:77015200-77015201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1011083	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011084	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152247	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851888	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10851889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072600	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072602	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072607	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072610	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072611	0.88[AMR][1000 genomes]
rs11072612	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072613	0.85[AMR][1000 genomes]
rs11072614	0.88[AMR][1000 genomes]
rs11072616	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072618	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072619	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072620	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072625	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072626	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072628	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072631	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11629727	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630185	0.83[AMR][1000 genomes]
rs11630402	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631082	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631394	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632670	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632765	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633309	0.85[AMR][1000 genomes]
rs11633869	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634266	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635162	0.85[AMR][1000 genomes]
rs11635273	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637096	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11637494	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852395	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852777	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11854850	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11855296	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855762	0.86[EUR][1000 genomes]
rs12437981	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12439141	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440511	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440691	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440965	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591622	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592686	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898416	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12898810	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904149	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904417	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905181	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910081	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910820	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913024	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914196	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915184	0.85[AMR][1000 genomes]
rs1443115	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484990	0.81[ASN][1000 genomes]
rs1603860	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1809875	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164102	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404604	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404734	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454451	0.81[EUR][1000 genomes]
rs28823285	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28895952	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103231	0.87[EUR][1000 genomes]
rs34215663	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34998733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35374222	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35710279	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36114653	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910756	0.88[AMR][1000 genomes]
rs4312276	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886816	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886819	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886823	0.84[AMR][1000 genomes]
rs4886837	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55746932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57682236	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60702982	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62026889	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026898	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178250	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7181506	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025991	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029283	0.83[EUR][1000 genomes]
rs920712	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635380	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs965818	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	esv3332270	chr15:77014424-77015725	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56339024	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs56339024	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76989600-77055800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:76990200-77025200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:76990400-77019000	Weak transcription	Fetal Kidney	kidney
4	chr15:76991000-77020400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:76992400-77056200	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:76992400-77056200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:76992600-77017200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:76992800-77017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:76992800-77056000	Weak transcription	Right Ventricle	heart
10	chr15:76993000-77017600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:76993000-77017800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:76993000-77020200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:76993000-77024800	Weak transcription	Gastric	stomach
14	chr15:76993000-77024800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:76993000-77024800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:76993000-77025000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:76993000-77025000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:76993200-77020200	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:76993200-77056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:76994200-77056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:76994800-77019000	Weak transcription	Placenta	Placenta
22	chr15:76994800-77020000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:76995800-77020400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:76996000-77017600	Weak transcription	Primary B cells from cord blood	blood
25	chr15:76996000-77025000	Weak transcription	Left Ventricle	heart
26	chr15:77007000-77017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:77007000-77020200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:77007000-77025000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:77007600-77029800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:77007800-77017200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:77008200-77019400	Weak transcription	Fetal Thymus	thymus
32	chr15:77008200-77020600	Weak transcription	Aorta	Aorta
33	chr15:77008200-77025200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:77008600-77017200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:77008600-77020600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:77008600-77020600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:77008600-77024800	Weak transcription	Pancreas	Pancrea
38	chr15:77008600-77025200	Weak transcription	Esophagus	oesophagus
39	chr15:77008600-77030000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:77008800-77017200	Weak transcription	Liver	Liver
41	chr15:77008800-77017200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:77008800-77019000	Weak transcription	Ovary	ovary
43	chr15:77008800-77020200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:77008800-77020600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:77008800-77020800	Weak transcription	Fetal Stomach	stomach
46	chr15:77008800-77037400	Weak transcription	Fetal Brain Male	brain
47	chr15:77009400-77017200	Weak transcription	Fetal Lung	lung
48	chr15:77010400-77017600	Weak transcription	Dnd41	blood
49	chr15:77011000-77017000	Weak transcription	Fetal Intestine Small	intestine
50	chr15:77011000-77017200	Weak transcription	Fetal Intestine Large	intestine

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