Variant report

Variant	rs1369666
Chromosome Location	chr3:160209026-160209027
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160195689..160198943-chr3:160208326..160210743,3	K562	blood:
2	chr3:160200027..160203201-chr3:160206463..160209183,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1047210	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10936203	0.81[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs11706810	0.92[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11718121	0.81[EUR][1000 genomes]
rs12630956	0.81[AFR][1000 genomes]
rs12632030	0.81[EUR][1000 genomes]
rs1451760	0.82[EUR][1000 genomes]
rs17236473	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17236544	0.82[CEU][hapmap]
rs17570467	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs17826221	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17826257	0.81[JPT][hapmap]
rs1882126	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs1882127	0.82[CEU][hapmap]
rs1920664	0.82[CEU][hapmap]
rs1971128	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123003	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3732706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773372	0.82[CEU][hapmap]
rs3851365	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851366	0.88[JPT][hapmap]
rs4679654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679888	0.80[ASN][1000 genomes]
rs4679890	0.81[CEU][hapmap]
rs4679891	0.81[CEU][hapmap]
rs4679895	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680589	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680591	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55992947	0.81[EUR][1000 genomes]
rs56156703	0.90[EUR][1000 genomes]
rs6768975	0.82[CEU][hapmap]
rs6785881	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6798183	0.92[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6798668	0.88[JPT][hapmap]
rs6808083	0.88[JPT][hapmap]
rs6809153	0.92[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs73875285	0.84[AFR][1000 genomes]
rs7618974	0.82[CEU][hapmap]
rs7620828	0.92[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7627555	0.92[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs7627756	0.82[CEU][hapmap]
rs7634826	0.88[JPT][hapmap]
rs7640072	0.88[JPT][hapmap]
rs7643779	0.82[CEU][hapmap]
rs7647873	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	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
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1369666	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160193400-160213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160199000-160211600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160204000-160211200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:160204000-160215800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:160204000-160216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:160204000-160219000	Weak transcription	Lung	lung
7	chr3:160204000-160219000	Weak transcription	Thymus	Thymus
8	chr3:160204000-160224000	Weak transcription	Gastric	stomach
9	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
10	chr3:160204200-160209600	Weak transcription	HSMMtube	muscle
11	chr3:160204200-160213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160204200-160215600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:160204200-160215800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160204200-160215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:160204200-160215800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:160204200-160215800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:160204200-160215800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:160204200-160215800	Weak transcription	Fetal Thymus	thymus
19	chr3:160204200-160215800	Weak transcription	HSMM	muscle
20	chr3:160204200-160215800	Weak transcription	NHDF-Ad	bronchial
21	chr3:160204200-160216000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:160204200-160216000	Weak transcription	Osteobl	bone
23	chr3:160204200-160216200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:160204200-160216200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:160204200-160216200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:160204200-160216200	Weak transcription	Liver	Liver
29	chr3:160204200-160216200	Weak transcription	HMEC	breast
30	chr3:160204200-160216400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:160204200-160216400	Weak transcription	HUVEC	blood vessel
32	chr3:160204200-160216800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:160204200-160217200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:160204200-160217600	Weak transcription	NH-A	brain
35	chr3:160204200-160218800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:160204200-160218800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:160204200-160219000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:160204200-160219000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:160204200-160219000	Weak transcription	NHEK	skin
40	chr3:160204200-160219200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:160204200-160219200	Weak transcription	Aorta	Aorta
42	chr3:160204200-160219200	Weak transcription	Left Ventricle	heart
43	chr3:160204200-160219400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:160204200-160224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:160204200-160224800	Weak transcription	GM12878-XiMat	blood
46	chr3:160204200-160225400	Weak transcription	Fetal Kidney	kidney
47	chr3:160204400-160215600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:160204400-160215800	Weak transcription	Primary B cells from cord blood	blood
49	chr3:160204400-160216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links