Variant report

Variant	rs11749262
Chromosome Location	chr5:35776239-35776240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10042935	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10941262	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10941264	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741496	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822736	0.84[ASW][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4869476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869618	0.89[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56163473	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56322028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56345129	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57276516	0.90[ASN][1000 genomes]
rs6883204	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6889260	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6895099	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72738869	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72738870	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11749262	LOC399744	trans	cerebellum	SCAN
rs11749262	UGT3A2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35771000-35781800	Weak transcription	Brain Anterior Caudate	brain
2	chr5:35772200-35777000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr5:35772200-35777400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:35772400-35777000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:35772400-35780600	Weak transcription	HSMM	muscle
6	chr5:35772800-35778000	Weak transcription	Fetal Thymus	thymus
7	chr5:35772800-35778000	Weak transcription	Thymus	Thymus
8	chr5:35774200-35776800	Weak transcription	HUVEC	blood vessel
9	chr5:35774200-35777000	Weak transcription	NHLF	lung
10	chr5:35774200-35777200	Weak transcription	Primary T cells from cord blood	blood
11	chr5:35774400-35777000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:35774400-35777200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:35774600-35776800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:35774600-35777000	Weak transcription	Osteobl	bone
15	chr5:35774600-35780800	Weak transcription	NHDF-Ad	bronchial
16	chr5:35774600-35781000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:35774800-35777000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:35775000-35779600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:35775200-35777000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:35775200-35777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:35775400-35776400	Weak transcription	Hela-S3	cervix
22	chr5:35775400-35777400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:35776000-35776800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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