Variant report

Variant	rs1500876
Chromosome Location	chr12:32659277-32659278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10506090	0.86[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10506093	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771960	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771961	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10771962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844223	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844224	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10844226	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10844227	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10844228	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10844229	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844230	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844231	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844234	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11052046	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11052052	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11052053	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11052055	0.81[MEX][hapmap]
rs11608343	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1500875	0.86[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17536908	0.81[MEX][hapmap]
rs2133943	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520681	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61928965	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7308163	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7962342	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964715	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7967306	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7967702	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7974089	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1500876	FGD4	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
2	chr12:32654400-32659400	Enhancers	HMEC	breast
3	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
4	chr12:32655200-32686000	Weak transcription	Lung	lung
5	chr12:32655400-32661000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:32656000-32661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
9	chr12:32656200-32659800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr12:32656200-32662600	Weak transcription	HepG2	liver
11	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:32656400-32659400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:32656400-32659400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:32656400-32659800	Enhancers	Fetal Lung	lung
15	chr12:32656400-32660000	Enhancers	Fetal Intestine Small	intestine
16	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:32656800-32659800	Enhancers	Fetal Intestine Large	intestine
18	chr12:32657000-32659600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:32657000-32659600	Enhancers	Psoas Muscle	Psoas
20	chr12:32657000-32661000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:32657000-32661800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:32657200-32659800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:32657200-32662200	Enhancers	Fetal Heart	heart
24	chr12:32657400-32659400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:32657400-32659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:32657400-32659600	Enhancers	Liver	Liver
27	chr12:32657400-32659800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:32657400-32661400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr12:32657600-32659400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:32657600-32659600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:32657800-32659600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:32658000-32659600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:32658000-32659600	Enhancers	Ovary	ovary
34	chr12:32658200-32659400	Enhancers	Fetal Kidney	kidney
35	chr12:32658200-32659600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:32658200-32659600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:32658200-32659800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:32658400-32659400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:32658400-32659600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:32658400-32659600	Enhancers	Brain Germinal Matrix	brain
41	chr12:32658400-32660400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:32658400-32660800	Weak transcription	Brain Angular Gyrus	brain
43	chr12:32658400-32660800	Weak transcription	Right Ventricle	heart
44	chr12:32658400-32661000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:32658600-32659400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:32658600-32659400	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:32658600-32659400	Active TSS	Fetal Brain Female	brain
48	chr12:32658600-32659800	Enhancers	Brain Anterior Caudate	brain
49	chr12:32658600-32659800	Enhancers	Brain Hippocampus Middle	brain
50	chr12:32658600-32660800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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