Variant report

Variant	rs1439901
Chromosome Location	chr2:189003106-189003107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

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	1.00[ASN][1000 genomes]
rs10469734	1.00[CHB][hapmap]
rs10931328	0.80[ASN][1000 genomes]
rs10931333	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931334	0.86[ASN][1000 genomes]
rs10931336	0.86[ASN][1000 genomes]
rs11682297	0.80[ASN][1000 genomes]
rs11687382	0.80[ASN][1000 genomes]
rs12465138	0.86[ASN][1000 genomes]
rs12478374	1.00[ASN][1000 genomes]
rs12615631	1.00[ASN][1000 genomes]
rs12693490	1.00[CHB][hapmap]
rs12693491	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs12693492	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs12693493	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs12693497	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs12990029	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992671	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12993224	0.82[ASN][1000 genomes]
rs12995107	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13003972	1.00[CHB][hapmap]
rs13005325	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13006933	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13011049	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13015608	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021054	1.00[ASN][1000 genomes]
rs13021984	1.00[ASN][1000 genomes]
rs13023212	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13027011	0.86[ASN][1000 genomes]
rs13027148	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13027989	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029662	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13032231	1.00[CHB][hapmap]
rs13382200	1.00[CHB][hapmap]
rs13390401	1.00[CHB][hapmap]
rs13394232	1.00[CHB][hapmap]
rs13403228	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs13429075	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs1371517	0.86[ASN][1000 genomes]
rs1371518	0.86[ASN][1000 genomes]
rs1371527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs1371528	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs1371529	1.00[ASN][1000 genomes]
rs1371530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1439894	0.86[ASN][1000 genomes]
rs1439898	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439905	0.86[ASN][1000 genomes]
rs1439909	1.00[ASN][1000 genomes]
rs16829628	1.00[CEU][hapmap]
rs16829839	1.00[ASN][1000 genomes]
rs2004888	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs2028374	1.00[ASN][1000 genomes]
rs2119091	0.86[ASN][1000 genomes]
rs2350563	1.00[ASN][1000 genomes]
rs2350566	0.80[ASN][1000 genomes]
rs2350569	0.83[ASN][1000 genomes]
rs2882449	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34142137	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34353529	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs34395949	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34511378	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34555222	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34699014	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34836837	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35113537	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35143496	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35311707	1.00[ASN][1000 genomes]
rs35355034	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35699394	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4128404	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs4427987	1.00[ASN][1000 genomes]
rs4535011	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs4666757	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667212	1.00[ASN][1000 genomes]
rs4667213	0.86[ASN][1000 genomes]
rs4667219	1.00[CHB][hapmap]
rs4667220	1.00[CHB][hapmap]
rs55755436	1.00[ASN][1000 genomes]
rs58176375	0.80[ASN][1000 genomes]
rs62180847	1.00[ASN][1000 genomes]
rs6434262	1.00[ASN][1000 genomes]
rs6434277	1.00[CHB][hapmap]
rs6707652	1.00[ASN][1000 genomes]
rs6707875	0.86[ASN][1000 genomes]
rs67082838	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6712945	1.00[ASN][1000 genomes]
rs6718697	1.00[CHB][hapmap]
rs6720983	1.00[CHB][hapmap]
rs6723998	1.00[ASN][1000 genomes]
rs6742606	0.86[ASN][1000 genomes]
rs67732490	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67804711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028976	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907984	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72909886	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72911800	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7565935	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7571197	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs7571494	1.00[CHB][hapmap]
rs920408	1.00[ASN][1000 genomes]
rs9288151	1.00[CHB][hapmap]
rs9288152	1.00[CHB][hapmap]
rs971268	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9808523	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs9808557	1.00[CHB][hapmap]
rs997044	0.89[ASN][1000 genomes]
rs997045	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533353	chr2:188498301-189024655	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875602	chr2:188923773-189016215	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv875603	chr2:188923773-189025977	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584044	chr2:188928433-189016215	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002714	chr2:188934297-189025084	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv584045	chr2:188949715-189003106	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv875604	chr2:188957640-189043137	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv584046	chr2:188967163-189006890	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1439901	COL3A1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188979400-189013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:189002400-189004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:189003000-189003600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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