Variant report

Variant	rs11714916
Chromosome Location	chr3:160400159-160400160
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: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936203	0.80[CEU][hapmap]
rs10936210	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11709300	0.81[ASN][1000 genomes]
rs11927913	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12639488	0.88[CEU][hapmap]
rs13065289	0.82[ASN][1000 genomes]
rs13095931	0.85[AMR][1000 genomes]
rs1403045	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522285	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16831337	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17236586	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1879797	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1882125	0.82[CEU][hapmap]
rs1980277	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2367209	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28544045	0.82[AMR][1000 genomes]
rs28730907	0.85[AMR][1000 genomes]
rs34362576	0.85[AMR][1000 genomes]
rs34444753	0.80[EUR][1000 genomes]
rs34949451	0.84[AMR][1000 genomes]
rs35308461	0.85[AMR][1000 genomes]
rs35480231	0.85[AMR][1000 genomes]
rs35498840	0.84[CEU][hapmap]
rs35867836	0.85[AMR][1000 genomes]
rs36118017	0.82[AMR][1000 genomes]
rs4133253	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4679659	0.82[AMR][1000 genomes]
rs4679660	0.85[AMR][1000 genomes]
rs4679909	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4679910	0.82[ASN][1000 genomes]
rs60339919	0.80[EUR][1000 genomes]
rs62272215	0.82[ASN][1000 genomes]
rs62272220	0.81[ASN][1000 genomes]
rs6763757	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6763892	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6773389	0.85[AMR][1000 genomes]
rs6773962	0.82[ASN][1000 genomes]
rs6776873	0.84[AMR][1000 genomes]
rs6777739	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6779581	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes]
rs6779671	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs6788429	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6788886	0.82[ASN][1000 genomes]
rs6792943	0.80[EUR][1000 genomes]
rs6797760	0.85[AMR][1000 genomes]
rs6798462	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6801373	0.85[AMR][1000 genomes]
rs6801636	0.82[ASN][1000 genomes]
rs6803670	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6806755	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7610939	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7632884	0.82[ASN][1000 genomes]
rs7633839	0.85[CEU][hapmap]
rs7634255	0.84[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11714916	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr3:160395800-160400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:160397000-160412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:160397200-160401800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:160397400-160400800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:160397400-160401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:160397400-160401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:160397400-160401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160397400-160403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:160397600-160401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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