Variant report

Variant	rs12988143
Chromosome Location	chr2:190354514-190354515
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	chr2:190353594..190356120-chr2:190357015..190358667,2	K562	blood:
2	chr2:190353445..190355042-chr2:190365324..190367722,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10187060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10497700	0.92[ASN][1000 genomes]
rs10497703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755004	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10931416	0.84[ASN][1000 genomes]
rs10931418	0.86[ASN][1000 genomes]
rs10931419	0.86[ASN][1000 genomes]
rs1112578	0.84[ASN][1000 genomes]
rs1157910	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs11677066	0.84[ASN][1000 genomes]
rs11688021	0.86[ASN][1000 genomes]
rs11695159	0.85[ASN][1000 genomes]
rs12612412	0.85[ASN][1000 genomes]
rs12613876	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12616234	0.84[ASN][1000 genomes]
rs12623723	0.84[ASN][1000 genomes]
rs12987962	0.98[ASN][1000 genomes]
rs12990035	0.84[ASN][1000 genomes]
rs12990235	0.84[ASN][1000 genomes]
rs12997620	0.86[ASN][1000 genomes]
rs13010531	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015203	0.91[ASN][1000 genomes]
rs13032853	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs13033841	0.86[ASN][1000 genomes]
rs1402368	0.86[ASN][1000 genomes]
rs1520855	0.85[ASN][1000 genomes]
rs1520857	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs1520864	0.84[ASN][1000 genomes]
rs1581351	0.88[ASN][1000 genomes]
rs2119069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304703	0.92[ASN][1000 genomes]
rs35997606	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4287797	0.86[ASN][1000 genomes]
rs4667281	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs6434339	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6728055	0.86[ASN][1000 genomes]
rs6745108	0.86[ASN][1000 genomes]
rs7419276	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7588453	0.84[ASN][1000 genomes]
rs7593821	0.88[ASN][1000 genomes]
rs7596592	0.86[ASN][1000 genomes]
rs963738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9679659	0.84[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	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12988143	COL3A1	cis	parietal	SCAN
rs12988143	COL5A2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190366200	Weak transcription	Ovary	ovary
2	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:190353000-190364600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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