Variant report

Variant	rs2074390
Chromosome Location	chr4:110910016-110910017
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	CEBPB	chr4:110910012-110910764	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
RNU6-35P	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10017564	0.83[AMR][1000 genomes]
rs10021804	0.81[AMR][1000 genomes]
rs11098057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11568904	0.82[AMR][1000 genomes]
rs12506702	0.82[AMR][1000 genomes]
rs12510173	0.83[AMR][1000 genomes]
rs12640600	0.81[AMR][1000 genomes]
rs1860129	0.87[AMR][1000 genomes]
rs2190907	0.86[AMR][1000 genomes]
rs2237049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237051	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237052	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237053	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282784	0.84[AMR][1000 genomes]
rs2298978	0.83[MEX][hapmap]
rs2298983	0.84[AMR][1000 genomes]
rs2298989	0.83[ASW][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes]
rs2298991	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2298992	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298993	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298999	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2347137	0.83[AMR][1000 genomes]
rs28471982	0.80[AMR][1000 genomes]
rs3796944	0.84[ASW][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs3796948	0.84[AMR][1000 genomes]
rs6533482	0.84[AMR][1000 genomes]
rs6533483	0.88[AMR][1000 genomes]
rs6533485	0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs6824594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825106	0.82[CHB][hapmap]
rs7692976	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs882405	0.84[AMR][1000 genomes]
rs882471	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929446	0.81[CEU][hapmap];0.86[AMR][1000 genomes]

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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2074390	GAR1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110895000-110928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110901000-110929600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110901400-110920800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:110902200-110910200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:110903200-110911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:110906800-110920800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:110907000-110932400	Weak transcription	Psoas Muscle	Psoas
8	chr4:110907800-110927400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:110908600-110916200	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:110909400-110910400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:110909600-110910200	Enhancers	Esophagus	oesophagus
12	chr4:110909600-110910200	Enhancers	Fetal Intestine Small	intestine
13	chr4:110909600-110910400	Enhancers	Hela-S3	cervix
14	chr4:110909600-110910400	Flanking Active TSS	NHEK	skin
15	chr4:110909600-110910600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:110909600-110910800	Enhancers	Fetal Heart	heart
17	chr4:110909600-110911200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr4:110909600-110912000	Enhancers	HMEC	breast
19	chr4:110909600-110913800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr4:110909800-110910400	Strong transcription	Pancreas	Pancrea
21	chr4:110909800-110910600	Enhancers	Right Atrium	heart
22	chr4:110909800-110911600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:110910000-110910200	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr4:110910000-110910200	Bivalent Enhancer	K562	blood
25	chr4:110910000-110910600	Enhancers	Placenta Amnion	Placenta Amnion

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