Variant report

Variant	rs10190976
Chromosome Location	chr2:234587442-234587443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234585462..234589750-chr2:234597767..234600526,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10199293	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477979	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602377	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602378	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602379	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602380	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741047	0.91[CEU][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741048	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741049	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741050	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433994	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583459	0.83[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4663888	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707947	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737107	0.91[CEU][hapmap]
rs6754100	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761246	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71405710	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7579530	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587916	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592624	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs7595138	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv3340677	chr2:234580879-234591324	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10190976	UGT1A9	cis	Esophagus Mucosa	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234554600-234587800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:234585400-234588000	Weak transcription	A549	lung
4	chr2:234585600-234589000	Weak transcription	Liver	Liver

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