Variant report

Variant	rs3102709
Chromosome Location	chr15:77072260-77072261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10431768	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10851890	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1114717	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442966	0.86[EUR][1000 genomes]
rs12593107	0.81[EUR][1000 genomes]
rs1398241	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1443110	0.87[EUR][1000 genomes]
rs166794	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1905694	0.92[EUR][1000 genomes]
rs1913001	0.83[EUR][1000 genomes]
rs2011635	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs203753	0.92[EUR][1000 genomes]
rs2046415	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063542	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170998	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439982	0.87[EUR][1000 genomes]
rs2439984	0.87[EUR][1000 genomes]
rs2454453	0.87[EUR][1000 genomes]
rs2468120	0.87[EUR][1000 genomes]
rs2468122	0.86[EUR][1000 genomes]
rs2468123	0.86[EUR][1000 genomes]
rs2585730	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629021	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629025	0.87[EUR][1000 genomes]
rs2629034	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs279997	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs279999	0.92[EUR][1000 genomes]
rs280000	0.80[EUR][1000 genomes]
rs280001	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280005	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280008	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280009	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280012	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280013	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280014	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280024	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280028	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280029	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280030	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs280033	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930681	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099134	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099137	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099138	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099140	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099142	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102710	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102712	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102713	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102714	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102716	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3106375	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3106377	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3106378	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3106380	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110378	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3110379	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110381	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110384	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35373913	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35645941	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4243043	0.82[EUR][1000 genomes]
rs4541044	0.83[EUR][1000 genomes]
rs4583202	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886828	0.82[ASN][1000 genomes]
rs4886831	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886832	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495222	0.83[EUR][1000 genomes]
rs7172639	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7174048	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7178759	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs901008	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3102709	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:78 , 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	chr15:77057000-77072600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:77057000-77074200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:77057000-77083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:77057000-77084600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:77057000-77084800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:77057000-77092000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:77057000-77097200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:77057200-77072400	Weak transcription	Right Ventricle	heart
10	chr15:77057200-77073000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:77057200-77098400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:77057800-77078000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:77057800-77098200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:77058000-77072400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:77058000-77072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:77058000-77083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:77058000-77083200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:77058000-77083200	Weak transcription	Fetal Thymus	thymus
19	chr15:77058000-77084000	Weak transcription	Fetal Heart	heart
20	chr15:77058000-77084400	Weak transcription	Left Ventricle	heart
21	chr15:77058000-77084800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:77058000-77084800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:77058000-77084800	Weak transcription	Fetal Kidney	kidney
24	chr15:77058000-77085600	Weak transcription	Thymus	Thymus
25	chr15:77058000-77100200	Weak transcription	Fetal Brain Male	brain
26	chr15:77058000-77106000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:77058200-77072400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:77058200-77072400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:77058200-77082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:77058200-77083400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:77058200-77084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:77058200-77084800	Weak transcription	Brain Substantia Nigra	brain
33	chr15:77058200-77085400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:77059000-77083000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:77059200-77078000	Weak transcription	Adipose Nuclei	Adipose
36	chr15:77065400-77085200	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:77067200-77084600	Weak transcription	Placenta	Placenta
38	chr15:77067400-77072400	Weak transcription	Liver	Liver
39	chr15:77067400-77083000	Weak transcription	Brain Anterior Caudate	brain
40	chr15:77067400-77083600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:77067400-77086000	Weak transcription	Brain Angular Gyrus	brain
42	chr15:77067600-77083400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:77068400-77072400	Weak transcription	Spleen	Spleen
44	chr15:77069200-77072400	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:77069200-77072400	Weak transcription	Pancreas	Pancrea
46	chr15:77069200-77072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:77069200-77072600	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:77069200-77085600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:77069400-77072400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:77069400-77072400	Weak transcription	Fetal Brain Female	brain

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