Variant report

Variant	rs12706772
Chromosome Location	chr7:126887802-126887803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr7:126887703-126887844	Hela-S3	cervix:	n/a	chr7:126887796-126887807
2	USF1	chr7:126887574-126888044	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:126884896..126891192-chr7:126891657..126895737,6	K562	blood:
2	chr7:126887307..126889755-chr7:127030651..127034460,3	MCF-7	breast:

Variant related genes	Relation type
GRM8	TF binding region
ENSG00000048405	Chromatin interaction
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10228722	0.91[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258076	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10487473	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs11563399	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11563675	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12706770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13222063	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13232203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246388	1.00[CHD][hapmap];0.86[MEX][hapmap]
rs1361936	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1592376	0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs17861434	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17862334	0.86[MEX][hapmap]
rs17863255	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17863256	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17863258	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17863264	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17866154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17867802	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17867811	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858776	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4731347	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs7777222	1.00[CHD][hapmap];0.93[MEX][hapmap]
rs7797094	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs950373	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs951640	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889189	chr7:126699088-126963028	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1819919	chr7:126850298-126888714	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv464712	chr7:126881029-126908258	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv608380	chr7:126881029-126908258	Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12706772	RBM28	cis	parietal	SCAN
rs12706772	KLHDC10	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126886000-126890400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:126887800-126890000	Weak transcription	Brain Hippocampus Middle	brain

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