Variant report

Variant	rs10513095
Chromosome Location	chr3:139736323-139736324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10935365	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715115	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11721080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895857	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4271881	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467410	0.88[CHB][hapmap]
rs4683466	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683794	0.86[CEU][hapmap]
rs55682807	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55722058	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55840308	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55982759	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56132049	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793464	0.94[CEU][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs73226905	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7625731	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9836664	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10513095	TXNDC6	cis	cerebellum	SCAN
rs10513095	GRK7	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139714400-139741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139727600-139737200	Weak transcription	Ovary	ovary
3	chr3:139732000-139739200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:139732400-139741200	Weak transcription	Fetal Brain Female	brain
5	chr3:139732400-139742600	Weak transcription	HSMMtube	muscle
6	chr3:139732800-139740200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:139733000-139739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:139734200-139739200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:139734400-139738800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:139735200-139738200	Weak transcription	Fetal Brain Male	brain
11	chr3:139736000-139741800	Weak transcription	Spleen	Spleen

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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