Variant report

Variant	rs12513242
Chromosome Location	chr4:103340510-103340511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103264289..103267173-chr4:103340178..103342964,2	MCF-7	breast:
2	chr4:103339972..103342129-chr4:103346957..103349862,2	MCF-7	breast:
3	chr4:103339552..103341633-chr4:103343792..103346168,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MANBA-1	chr4:103340421-103340516	ENSG00000248161.1
2	lnc-NFKB1-3	chr4:103340419-103340518	NONHSAT097586

Variant related genes	Relation type
ENSG00000138821	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11097781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097783	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12510679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12513230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115343	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13119968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13122985	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13132193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13132235	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13132722	0.85[EUR][1000 genomes]
rs13137839	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13150351	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150675	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17278473	0.82[TSI][hapmap]
rs17825737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17825838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2169595	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699028	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817730	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6846971	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs926163	1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12513242	HEATR7A	trans	cerebellum	SCAN
rs12513242	SLC39A8	cis	parietal	SCAN
rs12513242	UBE2D3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103325000-103341600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:103337800-103349800	Weak transcription	NHEK	skin
3	chr4:103338000-103342200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:103338400-103341600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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