Variant report

Variant	rs2298989
Chromosome Location	chr4:110891673-110891674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10014805	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10017564	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10021157	0.85[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs10025078	0.82[EUR][1000 genomes]
rs10025276	0.81[EUR][1000 genomes]
rs11098057	0.96[AMR][1000 genomes]
rs11568904	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12503113	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12506489	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12506702	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510173	0.89[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12640600	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1860129	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074390	0.83[ASW][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes]
rs2190907	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237040	0.81[EUR][1000 genomes]
rs2237049	0.83[ASW][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes]
rs2237051	0.83[ASW][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes]
rs2237052	0.82[CHB][hapmap];0.93[AMR][1000 genomes]
rs2237053	0.93[AMR][1000 genomes]
rs2282784	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2298978	0.81[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2298979	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2298983	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298991	0.87[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2298992	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2298993	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2347137	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2881559	0.85[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3796944	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796948	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4444903	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6533482	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533483	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533485	0.82[MEX][hapmap]
rs6824594	0.83[ASW][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes]
rs6855847	0.82[ASN][1000 genomes]
rs7692976	0.83[YRI][hapmap];0.91[AMR][1000 genomes]
rs882405	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs882471	0.87[GIH][hapmap];0.91[MEX][hapmap];0.95[AMR][1000 genomes]
rs929446	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298989	GAR1	cis	cerebellum	SCAN
rs2298989	AP1AR	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr4:110884200-110893600	Weak transcription	Fetal Heart	heart
4	chr4:110885800-110897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:110885800-110909800	Weak transcription	Left Ventricle	heart
6	chr4:110888200-110893800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:110889000-110891800	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:110889000-110894000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:110889400-110891800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:110890200-110894200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:110890200-110894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:110890400-110893600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:110890400-110894200	Weak transcription	NHEK	skin
14	chr4:110890400-110900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:110890600-110893800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:110890800-110891800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:110890800-110891800	Enhancers	HepG2	liver
18	chr4:110891000-110891800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:110891200-110891800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:110891200-110893200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:110891200-110900000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:110891400-110892800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:110891400-110893400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:110891400-110893800	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:110891600-110891800	Enhancers	Primary T cells from cord blood	blood
26	chr4:110891600-110891800	Enhancers	HUVEC	blood vessel
27	chr4:110891600-110891800	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr4:110891600-110892600	Weak transcription	Fetal Intestine Small	intestine
29	chr4:110891600-110895400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:110891600-110896400	Weak transcription	Spleen	Spleen

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