Variant report

Variant	rs16962440
Chromosome Location	chr15:49716845-49716846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11070692	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11634786	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439429	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1429556	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs1904316	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34813196	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4316697	0.90[CHB][hapmap]
rs6493361	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs6493363	0.80[CHB][hapmap]
rs7164109	0.85[EUR][1000 genomes]
rs8031480	0.83[JPT][hapmap];0.80[MEX][hapmap]
rs8034747	0.85[CHB][hapmap]
rs8040134	0.83[JPT][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16962440	COPS2	Cis_1M	lymphoblastoid	RTeQTL
rs16962440	LCMT2	cis	parietal	SCAN
rs16962440	SPATA5L1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49714000-49720400	Active TSS	Ovary	ovary
2	chr15:49714000-49720800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:49714000-49721000	Active TSS	Colon Smooth Muscle	Colon
4	chr15:49714000-49722600	Active TSS	Stomach Smooth Muscle	stomach
5	chr15:49714200-49718600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:49714200-49719400	Active TSS	Fetal Kidney	kidney
7	chr15:49714200-49721000	Active TSS	Rectal Smooth Muscle	rectum
8	chr15:49714200-49721000	Active TSS	Right Atrium	heart
9	chr15:49714200-49721400	Active TSS	Adipose Nuclei	Adipose
10	chr15:49714800-49720600	Active TSS	NHDF-Ad	bronchial
11	chr15:49715200-49717600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:49715200-49718000	Active TSS	Fetal Muscle Trunk	muscle
13	chr15:49715200-49718000	Active TSS	HSMMtube	muscle
14	chr15:49715200-49719200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr15:49715200-49719400	Active TSS	Fetal Muscle Leg	muscle
16	chr15:49715200-49719400	Active TSS	Right Ventricle	heart
17	chr15:49715200-49719600	Active TSS	Osteobl	bone
18	chr15:49715200-49720000	Active TSS	Fetal Stomach	stomach
19	chr15:49715400-49717600	Active TSS	Fetal Intestine Large	intestine
20	chr15:49715400-49718000	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr15:49715400-49718400	Active TSS	Fetal Intestine Small	intestine
22	chr15:49715400-49721600	Active TSS	NHLF	lung
23	chr15:49715800-49717000	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr15:49715800-49717400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:49715800-49718000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:49716000-49717600	Active TSS	Fetal Heart	heart
27	chr15:49716000-49718000	Active TSS	Fetal Lung	lung
28	chr15:49716200-49717000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:49716200-49732200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:49716400-49717000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:49716800-49717600	Weak transcription	Left Ventricle	heart
33	chr15:49716800-49720600	Weak transcription	Psoas Muscle	Psoas
34	chr15:49716800-49720600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:49716800-49720800	Weak transcription	Hela-S3	cervix
36	chr15:49716800-49722000	Weak transcription	Colonic Mucosa	Colon

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