Variant report

Variant	rs7303966
Chromosome Location	chr12:48320109-48320110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48296323..48299183-chr12:48320018..48324153,4	MCF-7	breast:
2	chr12:48303456..48306045-chr12:48319476..48321750,3	MCF-7	breast:
3	chr12:48116185..48118625-chr12:48317978..48320277,2	K562	blood:
4	chr12:48318671..48321191-chr12:48325244..48327910,3	K562	blood:

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10747525	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783221	0.93[ASW][hapmap];0.87[CEU][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875697	0.91[EUR][1000 genomes]
rs10875700	1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs10875701	0.91[EUR][1000 genomes]
rs10875702	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10875703	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875704	0.87[CEU][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10875705	0.80[EUR][1000 genomes]
rs10875706	0.89[EUR][1000 genomes]
rs10875707	0.89[EUR][1000 genomes]
rs10875708	0.87[CEU][hapmap];0.90[CHD][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10875709	0.89[EUR][1000 genomes]
rs11168307	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168308	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168310	0.84[EUR][1000 genomes]
rs11168311	0.93[EUR][1000 genomes]
rs11168313	0.80[EUR][1000 genomes]
rs11168314	0.87[CEU][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11168315	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs11168316	0.87[CEU][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11168318	0.87[CEU][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11168319	0.87[EUR][1000 genomes]
rs11168320	0.89[EUR][1000 genomes]
rs11568820	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11829292	0.91[EUR][1000 genomes]
rs12306963	0.83[EUR][1000 genomes]
rs12316950	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12831006	0.83[EUR][1000 genomes]
rs34381446	0.80[EUR][1000 genomes]
rs4237855	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4254129	0.91[EUR][1000 genomes]
rs4334089	0.81[JPT][hapmap]
rs4402365	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4411326	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs4442605	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4454781	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs61920869	0.82[EUR][1000 genomes]
rs61920870	0.91[EUR][1000 genomes]
rs71439418	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7300088	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300301	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305180	0.84[CHD][hapmap];0.82[EUR][1000 genomes]
rs7308216	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7970314	0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7975675	0.89[EUR][1000 genomes]
rs7976091	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7303966	C12orf54	cis	lymphoblastoid	seeQTL
rs7303966	AQP6	cis	cerebellum	SCAN
rs7303966	RAPGEF3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48318800-48323000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:48320000-48320200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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