Variant report

Variant	rs12471790
Chromosome Location	chr2:179196233-179196234
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	chr2:179182101..179184343-chr2:179194524..179196984,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10497513	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10497514	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10930829	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12151447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464380	0.86[GIH][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap]
rs12464536	0.96[ASN][1000 genomes]
rs12464806	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12467040	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12467053	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473890	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12474802	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12474844	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12474919	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12478760	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12478837	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12479027	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12479281	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618595	0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12618660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12620577	0.97[ASN][1000 genomes]
rs12620729	0.97[ASN][1000 genomes]
rs13400415	0.82[CHB][hapmap]
rs13402976	0.86[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs1368905	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1434082	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1434083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434084	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs1434086	0.96[ASN][1000 genomes]
rs1434089	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs16866231	0.85[CHB][hapmap]
rs16866256	1.00[ASN][1000 genomes]
rs16866271	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs16866272	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16866273	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866275	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866281	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866299	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1812550	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1836203	0.86[ASN][1000 genomes]
rs1982104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3813252	0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3813253	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4422196	0.86[ASN][1000 genomes]
rs4894008	0.81[EUR][1000 genomes]
rs4894011	0.86[ASN][1000 genomes]
rs4894012	0.88[EUR][1000 genomes]
rs4894013	0.86[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4894014	0.86[ASN][1000 genomes]
rs55989867	0.84[ASN][1000 genomes]
rs56148541	0.96[ASN][1000 genomes]
rs56366027	0.88[ASN][1000 genomes]
rs6433722	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6718010	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6754517	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6760059	0.86[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6761421	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs718650	0.97[ASN][1000 genomes]
rs718651	0.97[ASN][1000 genomes]
rs73032568	0.91[EUR][1000 genomes]
rs7559699	0.86[ASN][1000 genomes]
rs7559711	0.86[ASN][1000 genomes]
rs7572355	0.84[ASN][1000 genomes]
rs7576065	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7576231	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7576995	0.85[CHB][hapmap]
rs7587155	0.83[EUR][1000 genomes]
rs964165	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9646740	0.88[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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12471790	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
2	chr2:179176200-179198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
4	chr2:179185400-179198200	Weak transcription	Fetal Lung	lung
5	chr2:179189200-179196800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:179189200-179201200	Weak transcription	Ovary	ovary
7	chr2:179189400-179201200	Weak transcription	Fetal Brain Male	brain
8	chr2:179189800-179217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:179192600-179198600	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:179192600-179200600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:179193000-179201400	Weak transcription	NH-A	brain
12	chr2:179193000-179201800	Weak transcription	Fetal Kidney	kidney
13	chr2:179193000-179214600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:179193200-179199800	Enhancers	HSMMtube	muscle
15	chr2:179193200-179201000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:179193200-179201400	Weak transcription	Fetal Brain Female	brain
17	chr2:179193200-179210400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:179193200-179216200	Weak transcription	Adipose Nuclei	Adipose
19	chr2:179193400-179203400	Weak transcription	Fetal Intestine Small	intestine
20	chr2:179193400-179204800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:179193400-179215000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:179193600-179196600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:179194600-179229400	Weak transcription	K562	blood
24	chr2:179194800-179197200	Enhancers	HepG2	liver
25	chr2:179195000-179197000	Enhancers	Liver	Liver
26	chr2:179195000-179199200	Enhancers	HSMM	muscle
27	chr2:179195200-179196600	Enhancers	Brain Angular Gyrus	brain
28	chr2:179195200-179197000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:179195400-179214600	Weak transcription	Left Ventricle	heart
30	chr2:179195400-179229000	Weak transcription	Brain Substantia Nigra	brain
31	chr2:179195600-179214200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:179195600-179214800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:179195800-179196400	Flanking Active TSS	NHEK	skin
34	chr2:179195800-179197000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:179195800-179197000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:179195800-179197000	Enhancers	HMEC	breast
37	chr2:179195800-179198600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:179196000-179197000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:179196000-179197200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:179196000-179201000	Weak transcription	Brain Anterior Caudate	brain
41	chr2:179196200-179196400	Enhancers	Brain Germinal Matrix	brain
42	chr2:179196200-179196600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:179196200-179197000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:179196200-179207000	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links