Variant report

Variant	rs3986280
Chromosome Location	chr15:42850380-42850381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10454039	0.94[EUR][1000 genomes]
rs10518766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10851411	0.86[CEU][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs11022	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070374	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11631193	0.94[EUR][1000 genomes]
rs11636577	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324113	0.87[EUR][1000 genomes]
rs12324717	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12903432	0.89[EUR][1000 genomes]
rs12906697	0.94[EUR][1000 genomes]
rs16973174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1900921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241998	1.00[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs2255995	0.88[EUR][1000 genomes]
rs2595939	0.89[EUR][1000 genomes]
rs2595940	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2595941	0.87[EUR][1000 genomes]
rs2617236	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2899051	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899057	0.83[EUR][1000 genomes]
rs2899059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34643746	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs4573906	0.89[EUR][1000 genomes]
rs4923948	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924687	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7180483	1.00[ASN][1000 genomes]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302112	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3986280	TMCO5A	cis	parietal	SCAN
rs3986280	SNAP23	cis	parietal	SCAN
rs3986280	INO80	cis	parietal	SCAN
rs3986280	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs3986280	RINT1	trans	cerebellum	SCAN
rs3986280	MAP1A	cis	parietal	SCAN
rs3986280	MAP1A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42841600-42850800	Weak transcription	Pancreas	Pancrea
2	chr15:42841600-42851000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:42841600-42851200	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:42841600-42851600	Weak transcription	Lung	lung
5	chr15:42841600-42852000	Weak transcription	Gastric	stomach
6	chr15:42841600-42853600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:42841600-42854200	Weak transcription	Aorta	Aorta
8	chr15:42841600-42854200	Weak transcription	Esophagus	oesophagus
9	chr15:42841600-42854200	Weak transcription	Spleen	Spleen
10	chr15:42841600-42866800	Weak transcription	Stomach Mucosa	stomach
11	chr15:42841800-42850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:42841800-42857000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:42841800-42867000	Weak transcription	Ovary	ovary
14	chr15:42842200-42850400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:42842200-42850800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:42842200-42851000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:42842200-42851400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:42842200-42853000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:42842200-42854200	Weak transcription	Right Ventricle	heart
20	chr15:42842200-42856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:42842200-42867000	Weak transcription	Psoas Muscle	Psoas
22	chr15:42842400-42850400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:42842400-42850400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:42842400-42850600	Weak transcription	Fetal Intestine Small	intestine
25	chr15:42842400-42850800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:42842400-42850800	Weak transcription	HMEC	breast
27	chr15:42842400-42851000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:42842400-42851000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:42842400-42851000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:42842400-42851000	Weak transcription	Liver	Liver
31	chr15:42842400-42851000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:42842400-42851200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:42842400-42851400	Weak transcription	Placenta	Placenta
34	chr15:42842400-42851400	Weak transcription	Left Ventricle	heart
35	chr15:42842400-42851400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:42842400-42851400	Weak transcription	HSMMtube	muscle
37	chr15:42842400-42851600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:42842400-42851600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:42842400-42851600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:42842400-42851600	Weak transcription	NH-A	brain
41	chr15:42842400-42852000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:42842400-42853400	Weak transcription	HSMM	muscle
43	chr15:42842400-42854600	Weak transcription	A549	lung
44	chr15:42842400-42867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:42842600-42850600	Weak transcription	Thymus	Thymus
46	chr15:42842600-42850800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:42842600-42850800	Weak transcription	Adipose Nuclei	Adipose
48	chr15:42842600-42851000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:42842600-42851000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:42842600-42851200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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