Variant report

Variant	rs4869623
Chromosome Location	chr5:35772315-35772316
allele	A/G
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	MAFK	chr5:35771349-35772349	Hela-S3	cervix:	n/a	n/a
2	SMARCC1	chr5:35771313-35772873	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr5:35770772-35773113	Hela-S3	cervix:	n/a	chr5:35772052-35772064 chr5:35771698-35771707 chr5:35771698-35771707 chr5:35772945-35772956 chr5:35771698-35771707 chr5:35771696-35771709
4	USF2	chr5:35772159-35772760	Hela-S3	cervix:	n/a	chr5:35772575-35772586

Variant related genes	Relation type
SPEF2	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10037564	0.95[CHB][hapmap]
rs10043724	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap]
rs10043734	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10044393	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10941258	0.84[CHB][hapmap]
rs10941260	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs11957963	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12697350	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2201410	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs4869462	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869464	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62353695	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451213	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs6451217	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]
rs6451218	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875940	0.84[CHB][hapmap]
rs6891098	0.84[CHB][hapmap];0.85[TSI][hapmap]
rs716971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7443063	0.90[ASN][1000 genomes]
rs7447153	0.84[CHB][hapmap]
rs7705904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710255	0.84[CHB][hapmap];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4869623	TOMM7	cis	cerebellum	SCAN
rs4869623	UGT3A2	cis	parietal	SCAN
rs4869623	LOC149134	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35770000-35772800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:35770600-35772400	Enhancers	HSMM	muscle
3	chr5:35770600-35772400	Enhancers	NHDF-Ad	bronchial
4	chr5:35770600-35773000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:35770800-35772400	Flanking Active TSS	Hela-S3	cervix
6	chr5:35770800-35772600	Enhancers	NHLF	lung
7	chr5:35771000-35772400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:35771000-35781800	Weak transcription	Brain Anterior Caudate	brain
9	chr5:35771400-35772400	Enhancers	HSMMtube	muscle
10	chr5:35771400-35772400	Flanking Active TSS	Osteobl	bone
11	chr5:35771400-35773200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:35771600-35772600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:35771800-35772800	Enhancers	Primary T cells from cord blood	blood
14	chr5:35772000-35772400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:35772000-35772400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:35772000-35772800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:35772000-35774000	Weak transcription	HMEC	breast
18	chr5:35772200-35772600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:35772200-35772800	Enhancers	Fetal Thymus	thymus
20	chr5:35772200-35773800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:35772200-35774000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:35772200-35774000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:35772200-35777000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:35772200-35777400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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