Variant report

Variant	rs3099140
Chromosome Location	chr15:77111012-77111013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10431768	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851890	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1114717	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442966	0.81[EUR][1000 genomes]
rs12593107	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1398241	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443110	0.82[EUR][1000 genomes]
rs166794	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1813479	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1905694	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1913001	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2011635	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs203753	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2046415	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063542	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170998	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439982	0.82[EUR][1000 genomes]
rs2439984	0.82[EUR][1000 genomes]
rs2454453	0.82[EUR][1000 genomes]
rs2468120	0.82[EUR][1000 genomes]
rs2468122	0.81[EUR][1000 genomes]
rs2468123	0.81[EUR][1000 genomes]
rs2585730	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629021	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629025	0.82[EUR][1000 genomes]
rs2629034	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs279997	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs279999	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280001	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280005	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280008	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280009	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280012	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280013	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280014	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280024	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280028	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280029	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280030	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs280033	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930681	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099134	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099137	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099138	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099142	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099143	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102709	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102710	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102712	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102713	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3102714	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3102716	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3106375	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3106377	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3106378	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106380	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110378	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3110379	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110381	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110384	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35373913	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35645941	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243043	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4541044	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4583202	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886831	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886832	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886838	0.80[ASN][1000 genomes]
rs6495222	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7172639	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174048	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178759	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901008	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	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
6	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
7	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
8	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
9	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
rs3099140	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77073000-77125000	Weak transcription	Pancreas	Pancrea
2	chr15:77085400-77125000	Weak transcription	HSMM	muscle
3	chr15:77092800-77124800	Weak transcription	Ovary	ovary
4	chr15:77093200-77124800	Weak transcription	Primary B cells from cord blood	blood
5	chr15:77096200-77116400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:77096400-77113400	Weak transcription	Dnd41	blood
7	chr15:77096400-77116400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:77096600-77124800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:77097000-77113200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:77097000-77113200	Weak transcription	Primary T cells from cord blood	blood
11	chr15:77101200-77124800	Weak transcription	Aorta	Aorta
12	chr15:77105000-77113600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:77108000-77116600	Weak transcription	Left Ventricle	heart
14	chr15:77108000-77123600	Weak transcription	Psoas Muscle	Psoas
15	chr15:77108200-77123400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:77109400-77112000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:77110400-77111200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:77110400-77111400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:77111000-77111400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:77111000-77111600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:77111000-77111600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr15:77111000-77111600	ZNF genes & repeats	Fetal Stomach	stomach
23	chr15:77111000-77112000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr15:77111000-77112200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:77111000-77116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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