Variant report

Variant	rs13072556
Chromosome Location	chr3:160401027-160401028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160387401..160389689-chr3:160399672..160401960,2	K562	blood:
2	chr3:160396356..160398268-chr3:160398713..160401566,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10460866	0.90[EUR][1000 genomes]
rs11720693	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639488	0.87[CEU][hapmap]
rs13062928	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13075424	0.88[EUR][1000 genomes]
rs13085507	0.92[EUR][1000 genomes]
rs1403045	0.83[CEU][hapmap]
rs16831337	0.84[CEU][hapmap]
rs1879797	0.87[CEU][hapmap]
rs1882125	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2367209	0.85[EUR][1000 genomes]
rs34058107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34444753	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35498840	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4133253	0.84[CEU][hapmap]
rs57718211	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60339919	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792943	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806755	0.84[CEU][hapmap]
rs71314011	0.90[EUR][1000 genomes]
rs7610939	0.84[CEU][hapmap]
rs7633839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634255	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap];0.89[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13072556	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs13072556	IFT80	cis	parietal	SCAN
rs13072556	KLRB1	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160395600-160401600	Weak transcription	Gastric	stomach
2	chr3:160395600-160401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:160397000-160412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:160397200-160401800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:160397400-160401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:160397400-160401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:160397400-160401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160397400-160403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:160397600-160401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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