Variant report

Variant	rs2143349
Chromosome Location	chr6:56253790-56253791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56252910..56254417-chr6:56300788..56302600,2	MCF-7	breast:
2	chr6:56241738..56245167-chr6:56250105..56253808,4	MCF-7	breast:
3	chr6:56235606..56237147-chr6:56251903..56254247,2	MCF-7	breast:
4	chr6:56252890..56255029-chr6:56256865..56259570,2	MCF-7	breast:
5	chr6:56252272..56255163-chr6:56263455..56266276,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124749	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1008768	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1008769	0.85[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1008770	0.90[ASN][1000 genomes]
rs1014740	0.85[ASN][1000 genomes]
rs1018414	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1018415	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs11968073	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12205291	0.87[ASN][1000 genomes]
rs12528936	0.85[ASN][1000 genomes]
rs13206552	0.85[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2179519	0.88[ASN][1000 genomes]
rs2206528	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2206530	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[ASN][1000 genomes]
rs2397222	0.91[ASN][1000 genomes]
rs2894836	0.92[ASN][1000 genomes]
rs35253323	0.83[ASN][1000 genomes]
rs4715621	0.88[ASN][1000 genomes]
rs4715624	0.83[ASN][1000 genomes]
rs629057	0.88[ASN][1000 genomes]
rs629506	0.88[ASN][1000 genomes]
rs636389	0.81[CHB][hapmap]
rs643246	0.89[ASN][1000 genomes]
rs646884	0.85[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs669656	0.88[ASN][1000 genomes]
rs669728	0.88[ASN][1000 genomes]
rs926530	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9296843	0.85[ASN][1000 genomes]
rs9349821	0.85[ASN][1000 genomes]
rs9370527	0.85[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs9370530	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9382625	0.84[ASN][1000 genomes]
rs9382627	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9382630	0.83[ASN][1000 genomes]
rs9396208	0.85[ASN][1000 genomes]
rs9396209	0.85[ASN][1000 genomes]
rs9942454	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2143349	GCLC	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56247400-56263600	Weak transcription	Small Intestine	intestine
2	chr6:56251600-56253800	Enhancers	Liver	Liver
3	chr6:56252800-56253800	Enhancers	HepG2	liver
4	chr6:56253000-56282600	Weak transcription	Aorta	Aorta
5	chr6:56253200-56258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56253400-56253800	Enhancers	Hela-S3	cervix
7	chr6:56253400-56257000	Weak transcription	Left Ventricle	heart
8	chr6:56253600-56263000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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