Variant report

Variant	rs2731094
Chromosome Location	chr12:48881661-48881662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48880029..48882865-chr12:48884102..48887272,3	K562	blood:
2	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANP32D-2	chr12:48881610-48882283	NONHSAT028005

Variant related genes	Relation type
ENSG00000177627	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10747547	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168599	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168637	0.94[JPT][hapmap]
rs11458	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12371700	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12815544	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2114322	1.00[JPT][hapmap]
rs2731091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731092	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2731095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731097	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731099	0.84[CEU][hapmap]
rs2731102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2731106	0.80[CEU][hapmap]
rs2731107	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956467	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57444623	0.84[ASN][1000 genomes]
rs7139348	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs7294341	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7294585	0.84[CEU][hapmap]
rs7302209	0.85[ASN][1000 genomes]
rs7310960	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312017	0.89[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7958521	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7972785	0.83[ASN][1000 genomes]
rs7974213	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9268	0.83[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	nsv975484	chr12:48881500-48882416	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2731094	CCNT1	cis	cerebellum	SCAN
rs2731094	RPAP3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48880800-48882000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48880800-48882400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:48880800-48882400	Weak transcription	GM12878-XiMat	blood
4	chr12:48881000-48882800	Enhancers	NHEK	skin
5	chr12:48881600-48883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:48881600-48884000	Enhancers	HMEC	breast

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