Variant report

Variant	rs10880081
Chromosome Location	chr12:41884344-41884345
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10459287	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10506188	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10506193	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10748302	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10785269	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880086	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880089	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880091	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880093	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880095	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880096	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880097	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11180936	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180943	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180961	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180979	0.89[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11180981	0.89[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11180984	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11180988	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11180989	0.89[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11180994	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12229610	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12230775	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12372586	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458153	0.89[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs169564	1.00[JPT][hapmap]
rs17579291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[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]
rs1902908	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2054211	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2599254	0.82[JPT][hapmap]
rs2608709	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2730812	1.00[JPT][hapmap]
rs2730831	1.00[JPT][hapmap]
rs2730832	1.00[JPT][hapmap]
rs285551	1.00[JPT][hapmap]
rs285559	1.00[JPT][hapmap]
rs285586	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs285587	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs285588	1.00[JPT][hapmap]
rs285596	1.00[JPT][hapmap]
rs285597	1.00[JPT][hapmap]
rs287087	1.00[JPT][hapmap]
rs3110189	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725527	0.89[CEU][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73130674	0.88[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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10880081	SDC1	trans	lymphoblastoid	seeQTL
rs10880081	PDZRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41869600-41905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41877400-41903600	Weak transcription	Ovary	ovary
3	chr12:41881800-41887000	Weak transcription	Brain Germinal Matrix	brain

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