Variant report

Variant	rs7664587
Chromosome Location	chr4:79847536-79847537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10028067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061400	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs10857058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275046	0.94[CEU][hapmap]
rs1275047	0.94[CEU][hapmap]
rs1299129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108247	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs13122868	0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs13123305	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125525	0.90[ASN][1000 genomes]
rs13138117	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1426138	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs1480718	0.88[CEU][hapmap]
rs1871706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979444	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs2903600	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3937772	0.92[CEU][hapmap]
rs4246709	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512020	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs6534080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534083	0.89[CEU][hapmap]
rs6534090	0.85[MEX][hapmap]
rs6843690	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854347	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs7657727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664339	0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs7677084	0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs7690151	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7664587	LIN54	cis	cerebellum	SCAN
rs7664587	PRDM8	cis	parietal	SCAN
rs7664587	NAAA	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
2	chr4:79794200-79850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
4	chr4:79794400-79850000	Weak transcription	Pancreas	Pancrea
5	chr4:79794800-79850200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:79794800-79858000	Weak transcription	HepG2	liver
7	chr4:79799200-79858000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
9	chr4:79816000-79848200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:79816200-79848600	Weak transcription	Fetal Lung	lung
11	chr4:79816200-79858400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:79827400-79858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:79827400-79858000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:79829000-79859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:79830200-79850000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:79830200-79859200	Weak transcription	Hela-S3	cervix
17	chr4:79831000-79850000	Weak transcription	Gastric	stomach
18	chr4:79831200-79858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:79831400-79856600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:79833000-79849800	Weak transcription	Fetal Stomach	stomach
21	chr4:79833000-79850000	Weak transcription	Lung	lung
22	chr4:79833000-79850000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:79833000-79850000	Weak transcription	Spleen	Spleen
24	chr4:79833000-79850000	Weak transcription	HSMMtube	muscle
25	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
26	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
27	chr4:79833200-79848600	Weak transcription	Aorta	Aorta
28	chr4:79833200-79848600	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:79833200-79849800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:79833200-79849800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:79833200-79849800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:79833200-79849800	Weak transcription	Ovary	ovary
33	chr4:79833200-79850000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:79833200-79853400	Weak transcription	NHLF	lung
35	chr4:79833200-79859000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:79833200-79859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:79833400-79856800	Weak transcription	GM12878-XiMat	blood
38	chr4:79833600-79849000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:79833600-79849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:79833600-79858000	Weak transcription	Brain Substantia Nigra	brain
41	chr4:79833600-79859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:79833600-79859800	Weak transcription	Placenta	Placenta
43	chr4:79835600-79850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:79835600-79856000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:79836600-79848400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:79836600-79859000	Weak transcription	HSMM	muscle
47	chr4:79837000-79848800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:79839000-79848200	Weak transcription	Psoas Muscle	Psoas
49	chr4:79839000-79849600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:79839000-79850000	Weak transcription	Primary monocytes fromperipheralblood	blood

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