Variant report

Variant	rs7668455
Chromosome Location	chr4:533399-533400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:526650..530036-chr4:530929..534159,4	K562	blood:
2	chr4:498189..499885-chr4:532544..534324,2	K562	blood:

Variant related genes	Relation type
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10003485	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006279	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10014602	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014828	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10015083	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022506	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026805	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10027093	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10027174	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029096	0.85[CEU][hapmap]
rs10213007	0.87[CHB][hapmap];0.82[CHD][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs10213020	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11248023	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135945	0.83[JPT][hapmap]
rs11730410	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931543	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931692	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933478	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934533	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934538	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934549	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11936515	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936548	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936717	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936752	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938183	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940796	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940914	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944995	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946204	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105387	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13105652	0.81[EUR][1000 genomes]
rs13106068	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110171	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13111014	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114024	0.85[CEU][hapmap]
rs13114026	0.86[CEU][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs13115802	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13119658	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124714	0.86[CEU][hapmap]
rs13131404	0.85[CEU][hapmap]
rs13137203	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13141560	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146968	0.84[EUR][1000 genomes]
rs13149933	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150531	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs28380061	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28407137	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28458903	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28465192	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28465521	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28473153	0.88[ASN][1000 genomes]
rs28491533	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28535797	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28549216	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28624264	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28652818	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28673088	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28684815	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715137	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3211083	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247702	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34327839	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34584074	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34623004	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35122538	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35479345	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629431	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043622	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4324509	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4324510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4356866	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4380466	0.85[CEU][hapmap]
rs4488886	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4499656	0.85[CEU][hapmap]
rs4504200	0.85[CEU][hapmap]
rs55983970	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56121355	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59231873	0.96[ASN][1000 genomes]
rs59564702	1.00[ASN][1000 genomes]
rs61334630	1.00[ASN][1000 genomes]
rs6816690	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817963	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817973	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818642	0.92[CEU][hapmap]
rs6822767	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833031	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837492	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847050	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852371	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6855585	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72501954	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73072173	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072175	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072198	0.96[ASN][1000 genomes]
rs73792305	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73792306	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73794942	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7441980	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660555	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs7666226	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs7666425	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs7678962	0.86[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap]
rs7692313	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9884673	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884677	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884771	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884772	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884826	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS 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	44 gene(s)	inside rSNPs	diseases
4	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7668455	PIGG	cis	multi-tissue	Pritchard
rs7668455	C6orf35	trans	brain	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:494400-534600	Weak transcription	Fetal Heart	heart
2	chr4:495200-534000	Strong transcription	Fetal Stomach	stomach
3	chr4:506600-533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:506600-533600	Strong transcription	Liver	Liver
5	chr4:507200-533400	Strong transcription	Brain Anterior Caudate	brain
6	chr4:507400-533600	Strong transcription	Brain Hippocampus Middle	brain
7	chr4:507600-533600	Strong transcription	Brain Cingulate Gyrus	brain
8	chr4:510000-535400	Weak transcription	Hela-S3	cervix
9	chr4:514400-533400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:514600-533400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:518200-533800	Weak transcription	Psoas Muscle	Psoas
12	chr4:522800-535000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:523000-533600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:526200-534400	Weak transcription	HepG2	liver
15	chr4:526400-535000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:527800-534800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:528400-535000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:528800-533600	Strong transcription	Brain Angular Gyrus	brain
19	chr4:529000-535000	Weak transcription	Fetal Lung	lung
20	chr4:529800-542400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:530200-534400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:530800-533600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:530800-534400	Weak transcription	HMEC	breast
24	chr4:530800-534600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:530800-534800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:530800-535200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:530800-536000	Weak transcription	NHEK	skin
28	chr4:531000-533800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:531400-533600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:531400-533800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:531400-534400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:531600-533800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:531600-535000	Weak transcription	Brain Substantia Nigra	brain
34	chr4:531600-535400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:531800-533400	Weak transcription	Esophagus	oesophagus
36	chr4:531800-534400	Weak transcription	Thymus	Thymus
37	chr4:531800-534800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:531800-542600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:532000-533600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:532000-534000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:532000-534000	Weak transcription	Right Ventricle	heart
42	chr4:532000-534200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:532000-534600	Weak transcription	Dnd41	blood
44	chr4:532000-535000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:532000-535000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:532000-535600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:532000-535800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:532000-536200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:532000-537000	Weak transcription	Primary T cells from cord blood	blood
50	chr4:532200-534400	Weak transcription	Pancreas	Pancrea

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