Variant report

Variant	rs6441311
Chromosome Location	chr3:160035949-160035950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160031130..160033296-chr3:160034351..160037164,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10923	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10936201	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936203	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11708118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709232	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709336	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716413	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719750	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152435	0.82[EUR][1000 genomes]
rs12630564	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12630770	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630956	0.84[EUR][1000 genomes]
rs12638633	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12639488	0.82[EUR][1000 genomes]
rs16831207	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236494	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17826137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17826173	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17826257	0.82[EUR][1000 genomes]
rs1873076	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2095529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2099496	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2275151	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773369	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679886	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4679892	0.82[EUR][1000 genomes]
rs4680581	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680586	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56952700	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60395700	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875259	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73875285	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73875290	0.80[AMR][1000 genomes];0.82[EUR][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	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	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6441311	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
2	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
7	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
14	chr3:159999800-160047800	Weak transcription	Lung	lung
15	chr3:160010000-160047800	Weak transcription	HepG2	liver
16	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
19	chr3:160014800-160037200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:160015000-160044000	Weak transcription	Osteobl	bone
23	chr3:160015400-160048400	Weak transcription	A549	lung
24	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:160018000-160048600	Weak transcription	HSMM	muscle
26	chr3:160020600-160037600	Weak transcription	NH-A	brain
27	chr3:160021200-160043400	Weak transcription	NHDF-Ad	bronchial
28	chr3:160022400-160038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:160023000-160036800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:160023200-160037800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:160024400-160043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:160025400-160038800	Weak transcription	Liver	Liver
33	chr3:160025400-160056000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:160025600-160036200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:160025600-160048400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:160025600-160048600	Weak transcription	Brain Substantia Nigra	brain
38	chr3:160025600-160072000	Weak transcription	Thymus	Thymus
39	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
40	chr3:160026200-160047600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:160026600-160036400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:160027200-160036400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:160027800-160036000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:160029600-160050600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:160030200-160056000	Weak transcription	Fetal Stomach	stomach
46	chr3:160032000-160037800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:160033200-160037400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:160033200-160038400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:160033600-160036400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:160033800-160036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links