Variant report

Variant	rs12995564
Chromosome Location	chr2:11288577-11288578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11284108..11289562-chr2:11292670..11297251,9	MCF-7	breast:
2	chr2:11284894..11288705-chr2:11293327..11296838,5	MCF-7	breast:
3	chr2:11284657..11290990-chr2:11291519..11296260,8	K562	blood:

Variant related genes	Relation type
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10929723	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929724	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11676692	0.86[ASN][1000 genomes]
rs12612929	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617097	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12987119	0.84[ASN][1000 genomes]
rs12994920	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13000987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13022766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13028675	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13030385	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13031027	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828930	0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2037107	0.82[CEU][hapmap]
rs34315339	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34333866	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34344767	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34722769	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35536828	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36026430	0.86[ASN][1000 genomes]
rs3856468	0.86[CHB][hapmap]
rs4668714	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4669695	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55691236	0.84[ASN][1000 genomes]
rs55975936	0.86[ASN][1000 genomes]
rs6744659	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6754718	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6754745	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71439048	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs727803	0.86[ASN][1000 genomes]
rs72785431	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7581322	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7601782	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7605804	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7606827	0.85[ASN][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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12995564	C2orf50	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11273600-11294400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:11274000-11294600	Weak transcription	Right Atrium	heart
3	chr2:11284600-11294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11288000-11292000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:11288000-11294200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr2:11288200-11294400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:11288200-11294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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