Variant report

Variant	rs1058412
Chromosome Location	chr4:15513147-15513148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15507445..15508962-chr4:15512277..15514725,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10755215	0.90[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10939619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1125379	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11728800	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11931401	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500458	0.81[EUR][1000 genomes]
rs12508186	1.00[CHD][hapmap]
rs13131700	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17385493	0.90[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes]
rs1861048	0.81[CEU][hapmap]
rs2080176	0.81[CEU][hapmap]
rs2080177	0.81[CEU][hapmap]
rs28673332	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3087622	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33998592	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34465372	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4140933	0.81[CEU][hapmap]
rs4698112	0.81[CEU][hapmap]
rs4698114	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698387	0.85[EUR][1000 genomes]
rs4698395	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810461	0.81[CEU][hapmap]
rs6839217	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7675761	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998686	0.81[CEU][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1058412	C1QTNF7	cis	cerebellum	SCAN
rs1058412	FLJ39653	cis	cerebellum	SCAN
rs1058412	CPEB2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15519000	Weak transcription	Gastric	stomach
2	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:15482600-15526400	Weak transcription	HMEC	breast
5	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
7	chr4:15490400-15519400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:15490400-15539600	Weak transcription	Esophagus	oesophagus
9	chr4:15490600-15519000	Weak transcription	A549	lung
10	chr4:15491800-15516400	Weak transcription	NHLF	lung
11	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
12	chr4:15498200-15538400	Weak transcription	Fetal Heart	heart
13	chr4:15499000-15518200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:15499200-15515800	Weak transcription	Liver	Liver
15	chr4:15499600-15516600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:15499600-15528400	Weak transcription	Pancreas	Pancrea
17	chr4:15500200-15516800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:15500400-15523200	Weak transcription	NHEK	skin
19	chr4:15501400-15525400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr4:15501600-15519000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:15502000-15539400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:15502400-15525600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:15502400-15539400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:15502800-15517600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:15502800-15549200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
27	chr4:15503400-15516800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:15503600-15514400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:15503800-15519000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:15504000-15517600	Weak transcription	Brain Substantia Nigra	brain
31	chr4:15504000-15518800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:15504400-15519000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:15504400-15526800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr4:15505400-15516400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:15505600-15514800	Weak transcription	Left Ventricle	heart
36	chr4:15506600-15518200	Weak transcription	Fetal Brain Male	brain
37	chr4:15507000-15514000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:15507000-15515400	Weak transcription	Thymus	Thymus
39	chr4:15507600-15538200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:15507800-15518200	Weak transcription	Fetal Kidney	kidney
41	chr4:15508200-15513800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:15508200-15538600	Weak transcription	Primary T cells from cord blood	blood
43	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
44	chr4:15508400-15517000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:15508400-15518800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:15508400-15530000	Weak transcription	NHDF-Ad	bronchial
47	chr4:15508400-15530400	Weak transcription	NH-A	brain
48	chr4:15508800-15514600	Strong transcription	Fetal Intestine Large	intestine
49	chr4:15508800-15514800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr4:15508800-15545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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