Variant report

Variant	rs1401494
Chromosome Location	chr3:53696955-53696956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1037827	0.85[EUR][1000 genomes]
rs1380606	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599231	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1841291	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2250736	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2612022	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633707	0.88[AMR][1000 genomes]
rs2633731	0.92[CHB][hapmap]
rs2680654	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2680656	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3774472	1.00[YRI][hapmap]
rs3774486	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3774491	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6445591	0.82[EUR][1000 genomes]
rs6786135	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6809164	0.92[CHB][hapmap]
rs754063	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630805	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs898415	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs898416	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs930949	0.84[EUR][1000 genomes]
rs9883910	0.80[AMR][1000 genomes];0.87[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53677600-53700000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:53684800-53698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:53689600-53707400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:53692000-53707600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:53693600-53697600	ZNF genes & repeats	Liver	Liver
7	chr3:53694200-53699000	Strong transcription	Fetal Intestine Small	intestine
8	chr3:53694200-53699200	Strong transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:53694200-53700400	Strong transcription	Fetal Intestine Large	intestine
10	chr3:53694400-53701000	Weak transcription	Fetal Kidney	kidney
11	chr3:53695000-53697400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:53695800-53698600	Strong transcription	Fetal Lung	lung
13	chr3:53696000-53700200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:53696800-53706600	Weak transcription	Stomach Smooth Muscle	stomach

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