Variant report

Variant	rs7512467
Chromosome Location	chr1:10622374-10622375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10567319..10568120-chr1:10621986..10622609,2	K562	blood:
2	chr1:10615907..10618063-chr1:10619537..10622754,3	K562	blood:
3	chr1:10622081..10624385-chr1:10637309..10640742,3	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10157111	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10157119	0.86[EUR][1000 genomes]
rs10746495	0.89[EUR][1000 genomes]
rs10779739	0.86[EUR][1000 genomes]
rs10779744	0.90[JPT][hapmap]
rs10864461	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10864463	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10864465	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121584	0.86[EUR][1000 genomes]
rs11121585	0.83[EUR][1000 genomes]
rs11121588	0.89[EUR][1000 genomes]
rs11121589	0.89[EUR][1000 genomes]
rs11121594	0.90[JPT][hapmap]
rs11121596	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121597	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128630	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs12129678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403130	0.80[EUR][1000 genomes]
rs12565494	0.90[JPT][hapmap]
rs17035156	0.90[GIH][hapmap];0.90[MKK][hapmap]
rs2086650	0.90[JPT][hapmap]
rs2183377	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480771	0.86[EUR][1000 genomes]
rs2480772	1.00[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2480773	1.00[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2480775	0.92[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2480780	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480781	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2480786	0.86[GIH][hapmap]
rs2480789	0.85[GIH][hapmap]
rs2483678	0.90[GIH][hapmap]
rs2506878	0.85[GIH][hapmap]
rs2506887	0.91[GIH][hapmap]
rs2506897	0.84[EUR][1000 genomes]
rs2506898	0.84[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2506900	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2988398	0.83[EUR][1000 genomes]
rs2988399	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35612158	0.83[EUR][1000 genomes]
rs4240914	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240915	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs4845936	0.89[EUR][1000 genomes]
rs4846230	1.00[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs4846231	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4846232	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4846233	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs58788814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61777207	0.90[EUR][1000 genomes]
rs61777208	0.86[EUR][1000 genomes]
rs6540938	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6658073	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs6663688	0.90[JPT][hapmap]
rs6663898	0.89[JPT][hapmap]
rs6681221	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687502	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6700023	0.86[EUR][1000 genomes]
rs710130	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs72641424	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72641427	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747124	0.90[JPT][hapmap]
rs7536149	0.98[ASN][1000 genomes]
rs7545184	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944191	1.00[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs9660006	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][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	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1015079	chr1:10611403-10645176	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7512467	PEX14	cis	multi-tissue	Pritchard
rs7512467	POU3F1	trans	cerebellum	SCAN
rs7512467	VAMP3	cis	parietal	SCAN
rs7512467	MTHFR	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
2	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
3	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:10602000-10639600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:10602600-10624000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:10603000-10659000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:10604600-10623800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:10605000-10659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:10606000-10638000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:10607600-10623200	Weak transcription	Fetal Stomach	stomach
11	chr1:10607600-10636800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:10607600-10636800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:10607600-10641400	Weak transcription	Lung	lung
14	chr1:10609800-10624200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:10611800-10624000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:10614000-10623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:10616400-10623200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:10616400-10623400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:10616400-10633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:10616400-10638200	Weak transcription	Esophagus	oesophagus
21	chr1:10616600-10623200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:10616600-10626000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:10616800-10622400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:10616800-10627200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:10617000-10622600	Weak transcription	Adipose Nuclei	Adipose
26	chr1:10617000-10624200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:10617000-10627000	Weak transcription	HSMMtube	muscle
28	chr1:10621200-10622400	Enhancers	HMEC	breast
29	chr1:10621200-10622400	Enhancers	Osteobl	bone
30	chr1:10621200-10622800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:10621200-10623200	Weak transcription	Fetal Intestine Small	intestine
32	chr1:10621200-10624000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:10622000-10624000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:10622200-10622600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:10622200-10624000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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