Variant report

Variant	rs11721112
Chromosome Location	chr3:160289284-160289285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160156708..160158312-chr3:160288090..160290046,2	K562	blood:
2	chr3:160281906..160285341-chr3:160285654..160289811,8	MCF-7	breast:
3	chr3:160287495..160289317-chr3:160290381..160292497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10923	0.80[EUR][1000 genomes]
rs10936203	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11709232	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11711627	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11712392	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713230	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11716413	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12152435	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12630564	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12630956	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12638633	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12639488	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065269	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13074231	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075424	0.81[ASN][1000 genomes]
rs17236494	0.81[EUR][1000 genomes]
rs17826257	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920650	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1920663	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099496	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2123003	0.83[AFR][1000 genomes]
rs2141668	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2178451	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35008770	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679886	0.80[EUR][1000 genomes]
rs4679892	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679903	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679904	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680586	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56952700	0.80[EUR][1000 genomes]
rs73875285	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73875290	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7644186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
5	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11721112	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284200-160289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:160284800-160289600	Weak transcription	Fetal Lung	lung
3	chr3:160284800-160292000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
5	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:160285000-160289600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:160285000-160290800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:160285000-160292200	Weak transcription	Primary B cells from cord blood	blood
9	chr3:160285200-160289600	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:160285200-160293400	Weak transcription	HepG2	liver
11	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
12	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:160285800-160290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:160286800-160289800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:160286800-160290400	Weak transcription	Right Ventricle	heart
16	chr3:160286800-160291200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:160286800-160292800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:160286800-160294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:160286800-160295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:160286800-160295800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:160286800-160301200	Weak transcription	HMEC	breast
22	chr3:160287000-160289600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:160287000-160292000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:160287000-160292000	Weak transcription	Gastric	stomach
25	chr3:160287000-160293600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:160287000-160295600	Weak transcription	Adipose Nuclei	Adipose
27	chr3:160287200-160289600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:160287200-160290000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:160287200-160291800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:160287400-160291800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:160288000-160295400	Weak transcription	Psoas Muscle	Psoas
32	chr3:160288000-160295600	Weak transcription	Liver	Liver
33	chr3:160288200-160295600	Weak transcription	Muscle Satellite Cultured Cells	--

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