Variant report

Variant	rs10497668
Chromosome Location	chr2:187213730-187213731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10804005	0.82[ASN][1000 genomes]
rs1372649	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1375323	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827624	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16827719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17332860	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1868384	0.82[ASN][1000 genomes]
rs2083678	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2119861	0.92[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2119863	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2370663	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144784	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs55739229	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55770081	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56660382	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57092996	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57995640	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58438183	0.90[AMR][1000 genomes]
rs59376280	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60029175	0.87[AMR][1000 genomes]
rs60201574	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6717629	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6717871	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6730232	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719071	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs719072	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs72895450	0.91[ASN][1000 genomes]
rs73033491	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73033500	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73035219	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035226	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035248	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035254	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035266	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035270	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73035271	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73037534	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572647	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7577962	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7588772	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1006411	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536079	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv961744	chr2:187189976-187265519	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv3071	chr2:187208040-187252682	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10497668	ITGAV	cis	cerebellum	SCAN
rs10497668	ITGAV	cis	parietal	SCAN
rs10497668	ZSWIM2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187188600-187216200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:187207600-187213800	Weak transcription	Small Intestine	intestine
3	chr2:187207800-187214200	Weak transcription	Fetal Stomach	stomach
4	chr2:187208200-187219600	Weak transcription	Right Atrium	heart
5	chr2:187210600-187214400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:187211200-187214600	Enhancers	NHEK	skin
7	chr2:187211600-187214400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:187211600-187214600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:187211600-187214600	Enhancers	HMEC	breast
10	chr2:187211800-187214200	Enhancers	Fetal Lung	lung
11	chr2:187211800-187214400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:187211800-187214400	Enhancers	Colon Smooth Muscle	Colon
13	chr2:187211800-187214400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:187211800-187216200	Weak transcription	Ovary	ovary
15	chr2:187212000-187214200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:187212000-187214800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:187212000-187217600	Weak transcription	Psoas Muscle	Psoas
18	chr2:187212400-187214400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:187212400-187214600	Enhancers	HUVEC	blood vessel
20	chr2:187212600-187214400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:187212600-187214600	Enhancers	Stomach Mucosa	stomach
22	chr2:187212800-187213800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:187212800-187213800	Weak transcription	Hela-S3	cervix
24	chr2:187213000-187214200	Enhancers	Fetal Intestine Small	intestine
25	chr2:187213000-187214400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:187213200-187214000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:187213400-187214400	Enhancers	Duodenum Mucosa	Duodenum

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