Variant report

Variant	rs255351
Chromosome Location	chr5:94124220-94124221
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	NFIC	chr5:94124130-94124686	ECC-1	luminal epithelium:	n/a	chr5:94124409-94124425 chr5:94124410-94124427 chr5:94124411-94124427
2	NFIC	chr5:94124132-94124652	ECC-1	luminal epithelium:	n/a	chr5:94124409-94124425 chr5:94124410-94124427 chr5:94124411-94124427
3	NFIC	chr5:94124189-94124549	HepG2	liver:	n/a	chr5:94124409-94124425 chr5:94124410-94124427 chr5:94124411-94124427

Variant related genes	Relation type
ENSG00000249175	TF binding region
MCTP1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs153847	0.86[JPT][hapmap]
rs1549177	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs159602	0.87[JPT][hapmap]
rs185308	0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs185310	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs194256	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs194257	0.87[ASN][1000 genomes]
rs255212	0.87[JPT][hapmap]
rs255334	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs255335	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs255336	0.86[ASN][1000 genomes]
rs255337	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs255338	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs255340	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs255341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs255342	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs255343	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs255344	0.87[ASN][1000 genomes]
rs255345	0.87[ASN][1000 genomes]
rs255346	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs255347	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs255348	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs255349	1.00[ASN][1000 genomes]
rs255350	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs255352	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs255353	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs255367	0.87[JPT][hapmap]
rs255371	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs255373	0.83[ASN][1000 genomes]
rs255375	0.90[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs255376	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4143487	0.87[JPT][hapmap]
rs4869118	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs568600	0.93[JPT][hapmap]
rs7711390	0.84[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs255351	GPER	trans	lymphoblastoid	seeQTL
rs255351	MCTP1	cis	lymphoblastoid	seeQTL
rs255351	C5orf36	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94074200-94127600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:94083000-94125800	Weak transcription	HUVEC	blood vessel
3	chr5:94097800-94128400	Weak transcription	Primary T cells from cord blood	blood
4	chr5:94102200-94128000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:94104800-94128000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:94105200-94127800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:94106000-94126000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:94106000-94126000	Weak transcription	Lung	lung
9	chr5:94106400-94128800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:94112200-94128600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:94114400-94128200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:94114800-94124600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:94115400-94125600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:94120800-94127800	Weak transcription	GM12878-XiMat	blood
15	chr5:94122600-94129600	Weak transcription	Adipose Nuclei	Adipose
16	chr5:94122800-94128800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:94123000-94124600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:94123000-94124600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr5:94123400-94126000	Strong transcription	Fetal Thymus	thymus
20	chr5:94123800-94124400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:94124000-94124600	Enhancers	HepG2	liver
22	chr5:94124000-94124800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:94124000-94124800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:94124200-94124400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:94124200-94124800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:94124200-94127800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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