Variant report

Variant	rs57718211
Chromosome Location	chr3:160393110-160393111
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	chr3:160283415..160285026-chr3:160392303..160394437,2	MCF-7	breast:
2	chr3:160392640..160394500-chr3:160414229..160416051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207084	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10460866	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936210	0.80[EUR][1000 genomes]
rs11711627	0.80[ASN][1000 genomes]
rs11712392	0.82[ASN][1000 genomes]
rs11713230	0.82[ASN][1000 genomes]
rs11720693	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11927913	0.80[EUR][1000 genomes]
rs13062928	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065269	0.82[ASN][1000 genomes]
rs13072556	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13074231	0.82[ASN][1000 genomes]
rs13075424	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085507	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522285	0.81[EUR][1000 genomes]
rs16831337	0.80[EUR][1000 genomes]
rs1882125	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920650	0.80[ASN][1000 genomes]
rs1980277	0.81[EUR][1000 genomes]
rs2141668	0.80[ASN][1000 genomes]
rs2367209	0.90[EUR][1000 genomes]
rs34058107	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34444753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35008770	0.80[ASN][1000 genomes]
rs35498840	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679903	0.80[ASN][1000 genomes]
rs4679904	0.82[ASN][1000 genomes]
rs60339919	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6792943	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6803670	0.81[EUR][1000 genomes]
rs71314011	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610939	0.80[EUR][1000 genomes]
rs7633839	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7634255	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57718211	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160385200-160395000	Weak transcription	Colonic Mucosa	Colon
2	chr3:160386200-160393400	Weak transcription	Fetal Intestine Large	intestine
3	chr3:160389400-160393400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:160389400-160395200	Weak transcription	Pancreas	Pancrea
5	chr3:160389400-160395400	Weak transcription	Small Intestine	intestine
6	chr3:160390600-160393600	Enhancers	Stomach Mucosa	stomach
7	chr3:160391400-160394000	Enhancers	Liver	Liver
8	chr3:160391400-160395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:160391600-160393600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:160392000-160393400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:160392000-160394600	Enhancers	A549	lung
12	chr3:160392000-160395200	Weak transcription	HepG2	liver
13	chr3:160392400-160393400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:160392600-160393400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:160392800-160393200	Weak transcription	Rectal Mucosa Donor 31	rectum

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