Variant report

Variant	rs9292162
Chromosome Location	chr5:57799283-57799284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GAPT-1	chr5:57799122-57799527	NONHSAT101613

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10037721	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10039062	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10052714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10055153	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056153	0.85[CEU][hapmap]
rs10057028	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10063214	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064698	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064918	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069810	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070522	0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10071487	0.82[CHD][hapmap]
rs10472063	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10940616	0.82[JPT][hapmap]
rs1159072	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748206	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748233	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12186775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13178332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1389308	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1508908	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1508909	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508921	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559240	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1565729	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858086	0.98[ASN][1000 genomes]
rs1858087	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011644	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029690	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2408929	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2591918	0.86[CHD][hapmap]
rs2591919	0.82[CHD][hapmap]
rs4700294	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700295	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450479	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6872961	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879314	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6886814	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891070	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6892103	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892457	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704108	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708191	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710737	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717166	1.00[ASN][1000 genomes]
rs7721390	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721538	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722318	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726376	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9292163	0.96[ASN][1000 genomes]
rs9292164	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292167	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs963989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs966269	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966270	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9292162	GAPT	cis	Whole Blood	GTEx
rs9292162	FLJ33641	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57787400-57799400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:57788800-57801600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:57796200-57803200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:57796400-57800600	Weak transcription	Fetal Lung	lung
5	chr5:57796400-57800600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr5:57796400-57801400	Weak transcription	GM12878-XiMat	blood
7	chr5:57796800-57800800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:57797000-57800600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:57797000-57801400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:57797200-57801000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:57797800-57801800	Weak transcription	Primary T cells from cord blood	blood
12	chr5:57797800-57804200	Enhancers	Primary B cells from peripheral blood	blood
13	chr5:57798400-57801000	Enhancers	Primary B cells from cord blood	blood
14	chr5:57798800-57799600	Enhancers	Brain Germinal Matrix	brain
15	chr5:57798800-57799800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:57798800-57800600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:57798800-57804400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:57799200-57799400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:57799200-57799600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:57799200-57799800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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