Variant report

Variant	rs882471
Chromosome Location	chr4:110904973-110904974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110899444..110901234-chr4:110903435..110906853,3	MCF-7	breast:
2	chr4:110899256..110901567-chr4:110902882..110905571,2	K562	blood:
3	chr4:110903447..110905388-chr4:110907522..110909225,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10017564	0.83[AMR][1000 genomes]
rs11098057	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11568904	0.82[AMR][1000 genomes]
rs12506489	0.81[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]
rs2074390	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]
rs2190907	0.86[AMR][1000 genomes]
rs2237049	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237051	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237052	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237053	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282784	0.84[AMR][1000 genomes]
rs2298978	0.82[MEX][hapmap]
rs2298983	0.84[AMR][1000 genomes]
rs2298989	0.87[GIH][hapmap];0.91[MEX][hapmap];0.95[AMR][1000 genomes]
rs2298991	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2298992	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298993	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298999	0.81[CEU][hapmap]
rs2347137	0.83[AMR][1000 genomes]
rs3796944	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]
rs6824594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692976	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs882405	0.84[AMR][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
rs882471	GAR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110860600-110906600	Weak transcription	Psoas Muscle	Psoas
2	chr4:110875600-110909800	Weak transcription	Pancreas	Pancrea
3	chr4:110885800-110909800	Weak transcription	Left Ventricle	heart
4	chr4:110893800-110909600	Weak transcription	Fetal Heart	heart
5	chr4:110895000-110909600	Weak transcription	Fetal Intestine Small	intestine
6	chr4:110895000-110928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:110898000-110906600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:110899400-110909800	Weak transcription	Right Atrium	heart
9	chr4:110900800-110905000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:110901000-110905200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:110901000-110929600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:110901400-110920800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:110902000-110906800	Weak transcription	NHDF-Ad	bronchial
14	chr4:110902000-110907200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:110902200-110906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:110902200-110907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:110902200-110910200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:110902400-110909400	Weak transcription	NHEK	skin
19	chr4:110902600-110906800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:110902600-110906800	Weak transcription	HSMM	muscle
21	chr4:110902600-110909600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:110902800-110910000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:110903200-110911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:110904400-110906200	Weak transcription	HSMMtube	muscle
25	chr4:110904600-110906000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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