Variant report

Variant	rs17271015
Chromosome Location	chr2:190192867-190192868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190190556..190194601-chr2:190194832..190198444,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10174225	0.83[ASN][1000 genomes]
rs10177513	0.83[ASN][1000 genomes]
rs10497699	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs10497701	1.00[CEU][hapmap];0.87[AFR][1000 genomes]
rs10497702	1.00[MEX][hapmap]
rs10931402	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931406	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931410	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11675295	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11676812	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11677073	1.00[ASN][1000 genomes]
rs11678388	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11681937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684417	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684869	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11687908	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11690774	0.83[EUR][1000 genomes]
rs11693810	1.00[ASN][1000 genomes]
rs11695837	0.85[EUR][1000 genomes]
rs12472232	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1371470	0.84[AMR][1000 genomes]
rs1402369	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1515873	0.82[ASN][1000 genomes]
rs1515875	0.90[ASN][1000 genomes]
rs1519185	1.00[ASN][1000 genomes]
rs1520862	1.00[ASN][1000 genomes]
rs17198773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17198780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17198787	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17198815	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17198829	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17198857	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17198892	1.00[CEU][hapmap];0.87[AFR][1000 genomes]
rs17270952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17270966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17270973	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17270987	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17271008	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17271036	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17271043	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17271057	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs1996576	1.00[ASN][1000 genomes]
rs2289225	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs2304701	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2680629	0.83[ASN][1000 genomes]
rs2683013	1.00[ASN][1000 genomes]
rs2683014	1.00[ASN][1000 genomes]
rs2683015	0.83[ASN][1000 genomes]
rs2683016	0.83[ASN][1000 genomes]
rs28413975	0.93[ASN][1000 genomes]
rs35598715	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55822942	1.00[AFR][1000 genomes]
rs55851872	0.85[ASN][1000 genomes]
rs56252219	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56381644	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58584769	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58926658	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59031473	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61130121	0.93[ASN][1000 genomes]
rs61528955	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182060	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182061	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182067	0.83[ASN][1000 genomes]
rs62182068	1.00[ASN][1000 genomes]
rs62182069	1.00[ASN][1000 genomes]
rs62182415	0.87[ASN][1000 genomes]
rs62182421	0.87[ASN][1000 genomes]
rs62182457	0.85[ASN][1000 genomes]
rs62182458	0.82[ASN][1000 genomes]
rs62183794	0.87[ASN][1000 genomes]
rs62183841	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62183844	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62183845	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62183846	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183847	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183848	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62184647	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62184648	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62184649	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62184652	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62184653	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62187072	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62187074	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62187075	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6721290	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747132	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72908368	0.93[ASN][1000 genomes]
rs72908382	0.93[ASN][1000 genomes]
rs72910347	0.85[ASN][1000 genomes]
rs72912280	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72912286	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72914135	0.94[ASN][1000 genomes]
rs72914141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72914144	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72914175	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7423067	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7564429	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586853	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9636309	0.80[AMR][1000 genomes]
rs9808245	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17271015	COL5A2	cis	cerebellum	SCAN
rs17271015	COL5A2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190192000-190194200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:190192000-190194200	Enhancers	NHDF-Ad	bronchial
3	chr2:190192000-190194200	Enhancers	Osteobl	bone
4	chr2:190192200-190193800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:190192200-190194000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:190192200-190194200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:190192200-190194200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:190192600-190193000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:190192600-190193800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:190192600-190194000	Enhancers	NH-A	brain
11	chr2:190192600-190194200	Enhancers	HUVEC	blood vessel
12	chr2:190192800-190193200	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:190192800-190193400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:190192800-190193600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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