Variant report

Variant	rs6451217
Chromosome Location	chr5:35773777-35773778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr5:35773727-35774503	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr5:35773726-35774899	Hela-S3	cervix:	n/a	chr5:35774379-35774390 chr5:35774378-35774395 chr5:35774198-35774215

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35773670..35776063-chr5:35777809..35780068,2	K562	blood:

Variant related genes	Relation type
SPEF2	TF binding region
ENSG00000152582	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10037564	0.86[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10043724	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap]
rs10043734	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10044393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10941258	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs10941260	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11957963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12697350	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2201410	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4869462	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869623	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62353695	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451213	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875940	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs6891098	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap]
rs716971	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7443063	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7447153	0.84[CHB][hapmap]
rs7705904	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710255	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6451217	UGT3A2	cis	parietal	SCAN
rs6451217	LOC149134	trans	parietal	SCAN
rs6451217	LAG3	trans	lymphoblastoid	seeQTL
rs6451217	RICTOR	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35771000-35781800	Weak transcription	Brain Anterior Caudate	brain
2	chr5:35772000-35774000	Weak transcription	HMEC	breast
3	chr5:35772200-35773800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr5:35772200-35774000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:35772200-35774000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:35772200-35777000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:35772200-35777400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:35772400-35773800	Weak transcription	NHDF-Ad	bronchial
9	chr5:35772400-35775400	Enhancers	Hela-S3	cervix
10	chr5:35772400-35777000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:35772400-35780600	Weak transcription	HSMM	muscle
12	chr5:35772600-35773800	Weak transcription	NHLF	lung
13	chr5:35772800-35773800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:35772800-35773800	Weak transcription	Primary T cells from cord blood	blood
15	chr5:35772800-35773800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:35772800-35773800	Weak transcription	Osteobl	bone
17	chr5:35772800-35778000	Weak transcription	Fetal Thymus	thymus
18	chr5:35772800-35778000	Weak transcription	Thymus	Thymus
19	chr5:35773400-35774800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:35773600-35774400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:35773600-35775200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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