Variant report

Variant	rs1346037
Chromosome Location	chr15:62137911-62137912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-12	chr15:62137441-62138449	NONHSAT044260

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10851703	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10851704	0.90[YRI][hapmap]
rs10851705	0.84[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs11071634	0.82[CEU][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap]
rs11071635	0.82[CEU][hapmap]
rs11631013	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs11632842	0.83[JPT][hapmap]
rs11634516	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs11636504	0.80[ASN][1000 genomes]
rs11639482	0.81[CEU][hapmap]
rs12438431	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs12439934	0.85[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs12593844	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs12708468	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs12899801	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs12901171	0.80[ASN][1000 genomes]
rs12901247	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902092	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs12906423	0.80[EUR][1000 genomes]
rs12908081	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12908182	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909947	0.86[ASN][1000 genomes]
rs12910541	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12915825	0.81[EUR][1000 genomes]
rs12916268	0.81[EUR][1000 genomes]
rs13379947	0.82[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1344601	0.81[CEU][hapmap]
rs1346035	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346036	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1364810	0.89[YRI][hapmap]
rs1370177	0.83[JPT][hapmap]
rs1436965	0.83[JPT][hapmap]
rs1561197	0.83[JPT][hapmap]
rs17271158	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17271235	0.83[JPT][hapmap];0.80[YRI][hapmap]
rs17303968	0.82[JPT][hapmap]
rs17304010	0.86[JPT][hapmap];0.83[YRI][hapmap]
rs1981916	0.82[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1981917	0.81[EUR][1000 genomes]
rs1991205	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs2042608	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs2162062	0.81[CEU][hapmap]
rs2162064	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs2241491	0.81[CEU][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap]
rs2414755	0.82[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3210522	0.82[JPT][hapmap];0.90[YRI][hapmap]
rs3743294	0.90[YRI][hapmap]
rs3743297	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs3809517	0.81[CEU][hapmap]
rs3886246	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs4283171	0.81[EUR][1000 genomes]
rs4638519	0.85[JPT][hapmap]
rs4774425	0.82[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs4775442	0.82[CEU][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap]
rs4775444	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs4775445	0.83[JPT][hapmap]
rs4775447	0.82[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs4775453	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs6494299	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs6494300	0.90[JPT][hapmap];0.84[YRI][hapmap]
rs7163441	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs7164933	0.83[JPT][hapmap];0.90[YRI][hapmap]
rs7168164	0.82[JPT][hapmap]
rs7168715	0.87[ASN][1000 genomes]
rs8023668	0.90[JPT][hapmap]
rs8025282	0.82[ASN][1000 genomes]
rs8032433	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs8032681	0.82[EUR][1000 genomes]
rs8033816	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs8037603	0.82[JPT][hapmap];0.90[YRI][hapmap]
rs8038328	0.86[YRI][hapmap]
rs933807	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs9788670	0.86[YRI][hapmap]
rs9920945	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1346037	GTF2A2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62159000	Weak transcription	HSMM	muscle
2	chr15:62132400-62171200	Weak transcription	HMEC	breast
3	chr15:62132800-62146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:62134000-62144200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:62135000-62161600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:62136800-62150000	Weak transcription	HSMMtube	muscle
7	chr15:62137200-62144800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:62137400-62143400	Weak transcription	Adipose Nuclei	Adipose
9	chr15:62137400-62145400	Weak transcription	Liver	Liver

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