Variant report

Variant	rs2396570
Chromosome Location	chr7:112443541-112443542
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112442436..112445188-chr7:112575668..112578638,2	K562	blood:
2	chr7:112429306..112431701-chr7:112443388..112445678,2	MCF-7	breast:
3	chr7:112439935..112445178-chr7:112445414..112449539,5	K562	blood:

Variant related genes	Relation type
ENSG00000146802	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10228483	0.81[ASN][1000 genomes]
rs10238492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs10243834	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10249952	1.00[JPT][hapmap]
rs10272143	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10273589	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap]
rs10275208	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10280618	0.93[EUR][1000 genomes]
rs10280825	0.85[EUR][1000 genomes]
rs1044262	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11538991	0.81[ASN][1000 genomes]
rs11760733	0.81[ASN][1000 genomes]
rs11762737	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11768408	0.92[CEU][hapmap];0.82[CHD][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11768787	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11769037	0.82[EUR][1000 genomes]
rs1227163	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs1227174	0.82[CHB][hapmap]
rs1227181	0.82[CHB][hapmap]
rs1227190	0.82[CHB][hapmap]
rs1238698	0.82[CHB][hapmap]
rs1530756	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs17160078	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs17405723	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs1796492	0.82[CHB][hapmap]
rs1796493	0.82[CHB][hapmap]
rs1796516	0.82[CHB][hapmap]
rs1992988	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2285541	0.82[CHB][hapmap]
rs2396583	0.85[EUR][1000 genomes]
rs2457	0.82[CHB][hapmap]
rs2708296	0.82[CHB][hapmap]
rs3957315	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012709	0.84[EUR][1000 genomes]
rs62472534	0.86[ASN][1000 genomes]
rs6466421	0.82[CHB][hapmap]
rs6466423	0.97[EUR][1000 genomes]
rs6944843	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7777973	0.82[CHB][hapmap]
rs7781871	0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7803405	0.82[CHB][hapmap]
rs7806781	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs7808616	0.92[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv2752144	chr7:112398372-112499924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv967494	chr7:112430613-112445931	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv1031405	chr7:112431403-112476756	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv429801	chr7:112434049-112477049	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv2752145	chr7:112434049-112500049	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv1023222	chr7:112434413-112476756	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv1034863	chr7:112434413-112504160	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2396570	C7orf53	cis	parietal	SCAN
rs2396570	CAV2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112442800-112472800	Weak transcription	Lung	lung

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