Variant report

Variant	rs13413644
Chromosome Location	chr2:189475949-189475950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:189468156..189470886-chr2:189475486..189476986,2	MCF-7	breast:
2	chr2:189466156..189469106-chr2:189473632..189478313,4	MCF-7	breast:
3	chr2:189475431..189478005-chr2:189479402..189481105,2	MCF-7	breast:
4	chr2:189474730..189476735-chr2:189484207..189485935,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10153688	0.85[EUR][1000 genomes]
rs10153871	0.96[EUR][1000 genomes]
rs10172178	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173411	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10185750	1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs10199260	1.00[JPT][hapmap]
rs10203054	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10804021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10931363	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10931369	1.00[ASN][1000 genomes]
rs11679949	1.00[CEU][hapmap]
rs11683909	1.00[CEU][hapmap]
rs11683969	1.00[CEU][hapmap]
rs11685238	0.85[EUR][1000 genomes]
rs11685643	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs11693105	1.00[CEU][hapmap]
rs11695177	1.00[CEU][hapmap]
rs11695316	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902664	0.85[EUR][1000 genomes]
rs12463744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12475894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12476413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12997039	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13012993	1.00[ASN][1000 genomes]
rs13025659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13386581	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13392850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13393057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13397653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13412448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413752	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13418031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13424809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1354902	1.00[JPT][hapmap]
rs1354904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1354910	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1507551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567184	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1580993	1.00[ASN][1000 genomes]
rs1807235	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4453658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4577225	1.00[EUR][1000 genomes]
rs4667229	1.00[JPT][hapmap]
rs4667231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs55663622	0.85[EUR][1000 genomes]
rs61045757	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414119	0.85[EUR][1000 genomes]
rs6434285	0.85[EUR][1000 genomes]
rs6434286	0.89[EUR][1000 genomes]
rs66641143	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6707212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6722940	0.81[EUR][1000 genomes]
rs6727633	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67425558	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6744275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6756504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs698553	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7419798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7420808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7421510	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7422739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7423329	1.00[CEU][hapmap]
rs7423554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7568147	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7579593	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7582643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7587596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7596299	1.00[ASN][1000 genomes]
rs7602180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs781261	1.00[CHB][hapmap]
rs8273	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs9752583	0.80[EUR][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	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13413644	LRTM1	trans	brain	seeQTL
rs13413644	CRX	trans	brain	seeQTL
rs13413644	GUCA1C	trans	brain	seeQTL
rs13413644	ASMT	trans	brain	seeQTL
rs13413644	PDE6H	trans	brain	seeQTL
rs13413644	SLC5A7	trans	brain	seeQTL
rs13413644	SH2D2A	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189470800-189484000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:189472400-189476000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:189473400-189476200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:189473600-189476200	Enhancers	NHLF	lung
5	chr2:189474800-189476200	Enhancers	Adipose Nuclei	Adipose
6	chr2:189474800-189476400	Enhancers	Ovary	ovary
7	chr2:189475000-189476400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:189475400-189476200	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:189475800-189476000	Enhancers	Fetal Intestine Small	intestine

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