Variant report

Variant	rs12371700
Chromosome Location	chr12:48919213-48919214
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48917007..48919445-chr12:48952290..48954111,2	K562	blood:
2	chr12:48917515..48920061-chr12:49210634..49213027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198678	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10875827	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875829	0.97[EUR][1000 genomes]
rs10875833	0.91[EUR][1000 genomes]
rs11168577	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168586	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168599	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168618	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168619	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168637	0.87[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs11458	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425460	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs12815544	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2114322	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2731091	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2731094	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2731095	0.83[ASN][1000 genomes]
rs2731097	0.82[ASN][1000 genomes]
rs2731102	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2731107	0.83[ASN][1000 genomes]
rs2956467	0.81[ASN][1000 genomes]
rs35338015	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4359253	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57444623	0.96[ASN][1000 genomes]
rs6580671	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7301176	0.81[CHD][hapmap];0.84[MEX][hapmap]
rs7302209	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310960	0.81[ASN][1000 genomes]
rs7312017	0.94[JPT][hapmap]
rs7955785	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7972785	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974213	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976324	0.88[EUR][1000 genomes]
rs7980421	0.91[EUR][1000 genomes]
rs9268	0.92[CHB][hapmap]

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	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv1803653	chr12:48905575-48923774	Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12371700	CCNT1	cis	cerebellum	SCAN
rs12371700	ADAMTS20	cis	cerebellum	SCAN
rs12371700	OR10AD1	cis	cerebellum	SCAN
rs12371700	RPAP3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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