Variant report

Variant	rs2237049
Chromosome Location	chr4:110900791-110900792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110734994..110736731-chr4:110899705..110902509,2	K562	blood:
2	chr4:110899256..110901567-chr4:110902882..110905571,2	K562	blood:
3	chr4:110899444..110901234-chr4:110903435..110906853,3	MCF-7	breast:
4	chr4:110811671..110813373-chr4:110899497..110901188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272795	Chromatin interaction
ENSG00000109534	Chromatin interaction

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

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

rs_ID	r²[population]
rs10017564	0.84[AMR][1000 genomes]
rs10021804	0.80[AMR][1000 genomes]
rs11098057	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11568904	0.83[AMR][1000 genomes]
rs12506702	0.83[AMR][1000 genomes]
rs12510173	0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs12640600	0.82[AMR][1000 genomes]
rs1860129	0.88[AMR][1000 genomes]
rs2074390	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]
rs2190907	0.87[AMR][1000 genomes]
rs2237051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282784	0.85[AMR][1000 genomes]
rs2298978	0.87[MEX][hapmap]
rs2298983	0.85[AMR][1000 genomes]
rs2298989	0.83[ASW][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes]
rs2298991	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2298992	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298993	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298999	0.81[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap]
rs2347137	0.84[AMR][1000 genomes]
rs3796944	0.84[ASW][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes]
rs3796948	0.85[AMR][1000 genomes]
rs6533482	0.85[AMR][1000 genomes]
rs6533483	0.89[AMR][1000 genomes]
rs6533485	0.83[JPT][hapmap]
rs6824594	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7692976	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs882405	0.85[AMR][1000 genomes]
rs882471	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]
rs929446	0.81[CEU][hapmap];0.87[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
rs2237049	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	chr4:110890400-110900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:110893800-110909600	Weak transcription	Fetal Heart	heart
6	chr4:110894800-110900800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:110895000-110900800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:110895000-110909600	Weak transcription	Fetal Intestine Small	intestine
9	chr4:110895000-110928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:110898000-110906600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:110899400-110909800	Weak transcription	Right Atrium	heart
12	chr4:110899600-110900800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr4:110899600-110901000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr4:110899600-110902200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:110899600-110902200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:110899600-110902800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:110900000-110901400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:110900000-110901600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:110900000-110901600	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:110900200-110901000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:110900200-110901000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:110900200-110901200	Enhancers	NH-A	brain
23	chr4:110900400-110901600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr4:110900600-110900800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr4:110900600-110901000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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