Variant report

Variant	rs10931334
Chromosome Location	chr2:189058585-189058586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10175838	1.00[CHB][hapmap]
rs10180000	1.00[CHB][hapmap]
rs10189197	1.00[CHB][hapmap]
rs10209424	1.00[CHB][hapmap]
rs10460382	0.86[ASN][1000 genomes]
rs10469734	1.00[CHB][hapmap]
rs10931328	0.82[ASN][1000 genomes]
rs10931329	0.80[ASN][1000 genomes]
rs10931330	0.88[ASN][1000 genomes]
rs10931332	0.80[ASN][1000 genomes]
rs10931333	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682297	0.82[ASN][1000 genomes]
rs11684826	0.88[ASN][1000 genomes]
rs11687382	0.82[ASN][1000 genomes]
rs12465138	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468413	0.88[ASN][1000 genomes]
rs12478374	0.86[ASN][1000 genomes]
rs12615631	0.86[ASN][1000 genomes]
rs12693490	1.00[CHB][hapmap]
rs12693491	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12693492	1.00[CHB][hapmap]
rs12693493	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12693497	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12990029	0.80[ASN][1000 genomes]
rs12992671	0.81[ASN][1000 genomes]
rs12995107	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995166	0.88[ASN][1000 genomes]
rs12996638	0.91[ASN][1000 genomes]
rs13003972	1.00[CHB][hapmap]
rs13005325	0.80[AMR][1000 genomes]
rs13006933	0.80[ASN][1000 genomes]
rs13011049	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015608	0.86[ASN][1000 genomes]
rs13017543	0.80[ASN][1000 genomes]
rs13021054	0.86[ASN][1000 genomes]
rs13021984	0.86[ASN][1000 genomes]
rs13022215	0.88[ASN][1000 genomes]
rs13023212	0.86[ASN][1000 genomes]
rs13024023	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13027011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027148	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13027989	0.86[ASN][1000 genomes]
rs13029662	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13032231	1.00[CHB][hapmap]
rs13035864	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13382200	1.00[CHB][hapmap]
rs13390401	1.00[CHB][hapmap]
rs13394232	1.00[CHB][hapmap]
rs13403228	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs13429075	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1371517	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371518	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371526	0.85[ASN][1000 genomes]
rs1371527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs1371528	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs1371529	0.86[ASN][1000 genomes]
rs1371530	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1439888	0.86[ASN][1000 genomes]
rs1439889	0.86[ASN][1000 genomes]
rs1439894	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439898	0.86[ASN][1000 genomes]
rs1439900	0.86[ASN][1000 genomes]
rs1439901	0.86[ASN][1000 genomes]
rs1439903	0.88[ASN][1000 genomes]
rs1439904	0.80[ASN][1000 genomes]
rs1439905	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439909	0.86[ASN][1000 genomes]
rs16829628	0.83[CEU][hapmap]
rs16829839	0.86[ASN][1000 genomes]
rs1821998	0.88[ASN][1000 genomes]
rs2004888	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2028374	0.86[ASN][1000 genomes]
rs2043946	0.80[ASN][1000 genomes]
rs2119091	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119093	0.91[ASN][1000 genomes]
rs2218148	0.91[ASN][1000 genomes]
rs2350563	0.86[ASN][1000 genomes]
rs2350565	0.91[ASN][1000 genomes]
rs2350566	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2882449	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34142137	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34353529	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs34395949	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34555222	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34699014	0.80[ASN][1000 genomes]
rs34836837	0.86[ASN][1000 genomes]
rs35113537	0.86[ASN][1000 genomes]
rs35143496	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35311707	0.86[ASN][1000 genomes]
rs35355034	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35699394	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4128404	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs4427987	0.86[ASN][1000 genomes]
rs4450571	0.91[ASN][1000 genomes]
rs4535011	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs4666757	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667212	0.86[ASN][1000 genomes]
rs4667213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667219	1.00[CHB][hapmap]
rs4667220	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs55755436	0.86[ASN][1000 genomes]
rs58176375	0.82[ASN][1000 genomes]
rs62179560	0.80[ASN][1000 genomes]
rs62180847	0.86[ASN][1000 genomes]
rs6434262	0.86[ASN][1000 genomes]
rs6434277	1.00[CHB][hapmap]
rs6707652	0.86[ASN][1000 genomes]
rs6707875	1.00[ASN][1000 genomes]
rs67082838	0.80[ASN][1000 genomes]
rs6712945	0.86[ASN][1000 genomes]
rs6715740	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6718697	1.00[CHB][hapmap]
rs6720983	1.00[CHB][hapmap]
rs6723998	0.86[ASN][1000 genomes]
rs6726013	0.83[AFR][1000 genomes]
rs6726233	0.91[ASN][1000 genomes]
rs6729020	0.83[AFR][1000 genomes]
rs6738105	0.88[ASN][1000 genomes]
rs6742606	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744309	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745829	0.80[ASN][1000 genomes]
rs6749283	0.80[ASN][1000 genomes]
rs6749627	0.80[ASN][1000 genomes]
rs6756131	0.88[ASN][1000 genomes]
rs67732490	0.80[ASN][1000 genomes]
rs67804711	0.86[ASN][1000 genomes]
rs68028976	0.86[ASN][1000 genomes]
rs72907984	0.80[ASN][1000 genomes]
rs72909886	0.80[ASN][1000 genomes]
rs72911800	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7565935	0.80[ASN][1000 genomes]
rs7571197	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7571494	1.00[CHB][hapmap]
rs7582899	0.83[AFR][1000 genomes]
rs920408	0.86[ASN][1000 genomes]
rs9288151	1.00[CHB][hapmap]
rs9288152	1.00[CHB][hapmap]
rs971268	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9808523	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs9808557	1.00[CHB][hapmap]

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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv875605	chr2:189017499-189080087	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10931334	COL3A1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189046200-189061200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:189054400-189063600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:189056600-189058800	Enhancers	HMEC	breast
4	chr2:189057200-189058600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:189057600-189058600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:189057600-189058600	Enhancers	NHEK	skin
7	chr2:189057800-189058600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:189058400-189061200	Weak transcription	NH-A	brain

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