Variant report

Variant	rs35374222
Chromosome Location	chr15:77071394-77071395
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1011083	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011084	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10152247	0.82[EUR][1000 genomes]
rs10444809	0.85[ASN][1000 genomes]
rs10851889	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072607	0.80[EUR][1000 genomes]
rs11072610	0.82[EUR][1000 genomes]
rs11072612	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072616	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072618	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072619	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072620	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072628	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072631	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11629727	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11630402	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631082	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631394	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632365	0.85[AMR][1000 genomes]
rs11632670	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632765	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11633869	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634266	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634428	0.88[AMR][1000 genomes]
rs11635273	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11637096	0.82[EUR][1000 genomes]
rs11637296	0.85[AFR][1000 genomes]
rs11637494	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852777	0.80[EUR][1000 genomes]
rs11855296	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11855534	0.86[ASN][1000 genomes]
rs11855762	0.80[EUR][1000 genomes]
rs12439141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440511	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440691	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440965	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591622	0.81[EUR][1000 genomes]
rs12592686	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898416	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904149	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904417	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12905181	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910081	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910820	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913024	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913730	0.88[ASN][1000 genomes]
rs12914196	0.82[EUR][1000 genomes]
rs1443115	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1484990	0.89[ASN][1000 genomes]
rs1567671	0.85[AFR][1000 genomes]
rs1809875	0.81[EUR][1000 genomes]
rs2137311	0.88[ASN][1000 genomes]
rs2404604	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404734	0.81[EUR][1000 genomes]
rs28823285	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34103231	0.81[EUR][1000 genomes]
rs34215663	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34998733	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35710279	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36114653	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4312276	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886837	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55746932	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339024	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60702982	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62026889	0.80[EUR][1000 genomes]
rs62026898	0.82[EUR][1000 genomes]
rs62029232	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7165053	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178250	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181506	0.82[EUR][1000 genomes]
rs8025991	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs920712	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9635380	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
rs35374222	SCAPER	cis	Esophagus Muscularis	GTEx
rs35374222	SCAPER	cis	Artery Tibial	GTEx
rs35374222	SCAPER	cis	Adipose Subcutaneous	GTEx
rs35374222	SCAPER	cis	lung	GTEx
rs35374222	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs35374222	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs35374222	SCAPER	cis	Esophagus Mucosa	GTEx
rs35374222	SCAPER	cis	Whole Blood	GTEx
rs35374222	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs35374222	SCAPER	cis	Muscle Skeletal	GTEx
rs35374222	SCAPER	cis	Thyroid	GTEx
rs35374222	SCAPER	cis	Nerve Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77056800-77083400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:77057000-77072200	Weak transcription	Aorta	Aorta
3	chr15:77057000-77072200	Weak transcription	Esophagus	oesophagus
4	chr15:77057000-77072600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:77057000-77074200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:77057000-77083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:77057000-77084600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:77057000-77084800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:77057000-77092000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:77057000-77097200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:77057200-77072400	Weak transcription	Right Ventricle	heart
12	chr15:77057200-77073000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:77057200-77098400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:77057800-77078000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:77057800-77098200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:77058000-77072200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:77058000-77072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:77058000-77072200	Weak transcription	Ovary	ovary
19	chr15:77058000-77072400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:77058000-77072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:77058000-77083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:77058000-77083200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:77058000-77083200	Weak transcription	Fetal Thymus	thymus
24	chr15:77058000-77084000	Weak transcription	Fetal Heart	heart
25	chr15:77058000-77084400	Weak transcription	Left Ventricle	heart
26	chr15:77058000-77084800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:77058000-77084800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:77058000-77084800	Weak transcription	Fetal Kidney	kidney
29	chr15:77058000-77085600	Weak transcription	Thymus	Thymus
30	chr15:77058000-77100200	Weak transcription	Fetal Brain Male	brain
31	chr15:77058000-77106000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:77058200-77072400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:77058200-77072400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:77058200-77082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:77058200-77083400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:77058200-77084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:77058200-77084800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:77058200-77085400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:77059000-77083000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:77059200-77078000	Weak transcription	Adipose Nuclei	Adipose
41	chr15:77065400-77085200	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:77067200-77084600	Weak transcription	Placenta	Placenta
43	chr15:77067400-77072400	Weak transcription	Liver	Liver
44	chr15:77067400-77083000	Weak transcription	Brain Anterior Caudate	brain
45	chr15:77067400-77083600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:77067400-77086000	Weak transcription	Brain Angular Gyrus	brain
47	chr15:77067600-77083400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:77068400-77072400	Weak transcription	Spleen	Spleen
49	chr15:77069200-77072200	Weak transcription	Fetal Stomach	stomach
50	chr15:77069200-77072400	Weak transcription	Fetal Muscle Leg	muscle

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