Variant report

Variant	rs4679891
Chromosome Location	chr3:160246122-160246123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160243874..160245789-chr3:160246088..160248768,2	K562	blood:
2	chr3:160119557..160121442-chr3:160246035..160249000,2	K562	blood:
3	chr3:160245830..160248208-chr3:160254358..160256155,2	K562	blood:

Variant related genes	Relation type
ENSG00000113810	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10212236	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10513551	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs11706810	0.80[CEU][hapmap]
rs11918749	0.85[AMR][1000 genomes]
rs1317365	0.84[CEU][hapmap]
rs13403	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1451761	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1451762	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1451764	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1551190	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584688	0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236473	0.81[JPT][hapmap]
rs17236544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17570467	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882126	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920662	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279457	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305407	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2366969	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28705750	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886825	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732706	0.81[CEU][hapmap]
rs3732707	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851365	0.80[CEU][hapmap]
rs3851366	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4091703	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4292273	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4292274	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621370	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679655	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679885	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679888	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4679889	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679896	0.86[EUR][1000 genomes]
rs4679899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679900	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680579	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4680580	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4680585	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680587	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680588	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55731730	0.85[AMR][1000 genomes]
rs56156703	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56197102	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394279	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58322641	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60009222	0.83[AMR][1000 genomes]
rs60460891	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272792	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272794	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272800	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272810	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441314	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6441319	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6441320	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6768975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792612	0.83[AMR][1000 genomes]
rs6793560	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs6798668	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6801300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803828	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6806505	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808083	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6809153	0.80[CEU][hapmap]
rs6809313	0.80[CEU][hapmap]
rs721022	0.84[CEU][hapmap]
rs721023	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611130	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs7618974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627749	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627756	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7629202	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631792	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7634108	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7634826	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7640072	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644453	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645832	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869468	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9798898	0.85[AMR][1000 genomes]
rs9862595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9968151	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv877700	chr3:160223172-160248363	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679891	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:160216200-160249200	Strong transcription	Liver	Liver
7	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:160217200-160254000	Strong transcription	Dnd41	blood
11	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
13	chr3:160220600-160246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
15	chr3:160221600-160249000	Strong transcription	HUVEC	blood vessel
16	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
17	chr3:160229000-160253400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:160229200-160247000	Strong transcription	Adipose Nuclei	Adipose
19	chr3:160229200-160252800	Strong transcription	Fetal Thymus	thymus
20	chr3:160229200-160253400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:160229200-160253400	Strong transcription	Osteobl	bone
22	chr3:160229200-160253600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:160229200-160254000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:160229200-160254000	Strong transcription	Placenta	Placenta
25	chr3:160229600-160253400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:160229600-160253600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:160229800-160253200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:160229800-160253400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:160229800-160253600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:160229800-160253600	Strong transcription	HSMM	muscle
31	chr3:160229800-160253800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:160230000-160249800	Strong transcription	Fetal Intestine Large	intestine
33	chr3:160230000-160252800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:160230000-160253000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:160230000-160253600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:160230000-160254000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:160230200-160253600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:160230400-160253000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:160230400-160253200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:160230400-160253400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:160230600-160247200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:160230600-160248800	Strong transcription	Primary T cells from cord blood	blood
43	chr3:160230600-160249400	Strong transcription	Primary B cells from cord blood	blood
44	chr3:160230600-160253400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:160230600-160254600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:160231000-160251000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr3:160231000-160254400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:160231400-160247000	Strong transcription	NHDF-Ad	bronchial
49	chr3:160234200-160258200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:160234600-160246200	Weak transcription	Gastric	stomach

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