Variant report

Variant	rs4133253
Chromosome Location	chr3:160396459-160396460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160396356..160398268-chr3:160398713..160401566,2	MCF-7	breast:
2	chr3:160392050..160395141-chr3:160395142..160398552,4	K562	blood:
3	chr3:160395173..160398062-chr3:160414143..160415987,2	K562	blood:
4	chr3:160395405..160397806-chr3:160539467..160541973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179674	Chromatin interaction
ENSG00000207084	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10936203	0.80[CEU][hapmap]
rs10936207	0.87[ASN][1000 genomes]
rs10936208	0.86[ASN][1000 genomes]
rs10936209	0.87[ASN][1000 genomes]
rs10936210	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11927913	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490985	0.80[ASN][1000 genomes]
rs12639488	0.88[CEU][hapmap]
rs13095931	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1317085	0.87[ASN][1000 genomes]
rs1403045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522285	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831337	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236586	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1879797	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882125	0.82[CEU][hapmap]
rs1980277	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178452	0.87[ASN][1000 genomes]
rs2367209	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28544045	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28730907	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34362576	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34949451	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35308461	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35480231	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35498840	0.84[CEU][hapmap]
rs35664264	0.87[ASN][1000 genomes]
rs35867836	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36118017	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4679659	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4679660	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4679909	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs62272216	0.87[ASN][1000 genomes]
rs62272217	0.87[ASN][1000 genomes]
rs62272218	0.87[ASN][1000 genomes]
rs62272219	0.81[ASN][1000 genomes]
rs62272220	0.88[ASN][1000 genomes]
rs6763757	0.83[AMR][1000 genomes]
rs6763892	0.83[AMR][1000 genomes]
rs6773389	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6774379	0.87[ASN][1000 genomes]
rs6774566	0.87[ASN][1000 genomes]
rs6776873	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6777739	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6779581	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6779671	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6787452	0.87[ASN][1000 genomes]
rs6788429	0.83[AMR][1000 genomes]
rs6797760	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6798462	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6801373	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6803670	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610939	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633839	0.85[CEU][hapmap]
rs7634255	0.84[CEU][hapmap]

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
rs4133253	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160393400-160397000	Enhancers	HMEC	breast
2	chr3:160393400-160397200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:160393400-160397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:160394200-160397400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:160394400-160396800	Enhancers	HUVEC	blood vessel
6	chr3:160394400-160397400	Active TSS	Stomach Mucosa	stomach
7	chr3:160394600-160397400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:160394800-160396600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:160394800-160396600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:160394800-160397800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:160395000-160396600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:160395000-160396600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:160395000-160397200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:160395000-160397400	Active TSS	Colonic Mucosa	Colon
15	chr3:160395000-160397600	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr3:160395000-160398000	Active TSS	Duodenum Mucosa	Duodenum
17	chr3:160395200-160396800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:160395200-160397000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:160395200-160397000	Active TSS	Pancreas	Pancrea
20	chr3:160395200-160397400	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:160395200-160397600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:160395200-160397800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:160395400-160396600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:160395400-160396600	Enhancers	Fetal Lung	lung
25	chr3:160395400-160397000	Enhancers	Fetal Muscle Leg	muscle
26	chr3:160395600-160397200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:160395600-160397400	Enhancers	NHEK	skin
28	chr3:160395600-160397800	Enhancers	Hela-S3	cervix
29	chr3:160395600-160401600	Weak transcription	Gastric	stomach
30	chr3:160395600-160401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:160395800-160396600	Active TSS	Fetal Intestine Small	intestine
32	chr3:160395800-160396600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:160395800-160396800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:160395800-160396800	Weak transcription	Small Intestine	intestine
35	chr3:160395800-160400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:160396200-160396600	Active TSS	Fetal Intestine Large	intestine
37	chr3:160396200-160396600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:160396200-160396800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr3:160396200-160396800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:160396200-160396800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:160396200-160396800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr3:160396200-160397000	Flanking Active TSS	Fetal Stomach	stomach
43	chr3:160396200-160397200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:160396200-160397600	Enhancers	A549	lung
45	chr3:160396400-160396600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:160396400-160396600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:160396400-160396600	Enhancers	HepG2	liver
48	chr3:160396400-160396800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:160396400-160396800	Flanking Active TSS	Fetal Kidney	kidney

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