Variant report

Variant	rs2170998
Chromosome Location	chr15:77007159-77007160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10431768	0.81[EUR][1000 genomes]
rs10851890	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1114717	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442966	0.91[EUR][1000 genomes]
rs1398241	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1443110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157768	0.87[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap]
rs157769	0.86[CEU][hapmap]
rs166794	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1905694	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011635	0.85[EUR][1000 genomes]
rs203753	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2046415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2063542	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439982	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439989	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439991	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2439993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs2454453	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2459360	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2459363	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2468116	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2468120	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2468122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2468123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2468129	0.82[EUR][1000 genomes]
rs2469242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2469244	0.96[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap]
rs2585730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629021	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2629034	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs279997	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs279999	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280000	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs280001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280005	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280008	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280009	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280014	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280029	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280030	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs280033	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099138	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099140	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099142	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099143	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3102709	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3102710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3102712	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3102713	0.86[EUR][1000 genomes]
rs3102714	0.90[EUR][1000 genomes]
rs3102716	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3106375	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3106377	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3106378	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3106380	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3110378	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3110379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3110381	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3110384	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35373913	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35645941	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35994108	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4541044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4583202	0.81[EUR][1000 genomes]
rs4886828	0.82[AFR][1000 genomes]
rs4886831	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886838	0.89[ASW][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap]
rs494268	0.87[CEU][hapmap]
rs506000	0.87[CEU][hapmap]
rs7172639	0.81[EUR][1000 genomes]
rs7174048	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7178759	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs901008	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2170998	C15orf60	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76984200-77008200	Weak transcription	Fetal Lung	lung
2	chr15:76989600-77055800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:76990200-77025200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:76990400-77019000	Weak transcription	Fetal Kidney	kidney
5	chr15:76991000-77020400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:76991200-77007600	Weak transcription	Fetal Brain Male	brain
7	chr15:76992400-77056200	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:76992400-77056200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:76992600-77017200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:76992800-77007400	Weak transcription	Thymus	Thymus
11	chr15:76992800-77008400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:76992800-77017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:76992800-77056000	Weak transcription	Right Ventricle	heart
14	chr15:76993000-77007400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:76993000-77007400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:76993000-77007400	Weak transcription	Esophagus	oesophagus
17	chr15:76993000-77007400	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:76993000-77007400	Weak transcription	Fetal Stomach	stomach
19	chr15:76993000-77007400	Weak transcription	Ovary	ovary
20	chr15:76993000-77007400	Weak transcription	Pancreas	Pancrea
21	chr15:76993000-77007600	Weak transcription	Aorta	Aorta
22	chr15:76993000-77007800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:76993000-77007800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:76993000-77009200	Weak transcription	Brain Anterior Caudate	brain
25	chr15:76993000-77010200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:76993000-77017600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:76993000-77017800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:76993000-77020200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:76993000-77024800	Weak transcription	Gastric	stomach
30	chr15:76993000-77024800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:76993000-77024800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:76993000-77025000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:76993000-77025000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:76993200-77007600	Weak transcription	Fetal Brain Female	brain
35	chr15:76993200-77007800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:76993200-77008000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:76993200-77020200	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:76993200-77056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:76993400-77007600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:76994200-77007400	Weak transcription	Brain Germinal Matrix	brain
41	chr15:76994200-77056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:76994600-77007400	Weak transcription	Brain Angular Gyrus	brain
43	chr15:76994800-77019000	Weak transcription	Placenta	Placenta
44	chr15:76994800-77020000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:76995000-77007200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:76995200-77007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:76995200-77008200	Weak transcription	Adipose Nuclei	Adipose
48	chr15:76995400-77007400	Weak transcription	Liver	Liver
49	chr15:76995400-77007600	Weak transcription	Dnd41	blood
50	chr15:76995800-77020400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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