Variant report

Variant	rs12404263
Chromosome Location	chr1:84551736-84551737
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	chr1:84551652..84556823-chr1:84558383..84561144,5	K562	blood:
2	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:

Variant related genes	Relation type
ENSG00000142875	Chromatin interaction
ENSG00000271576	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1021490	0.86[AMR][1000 genomes]
rs10493750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[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];0.95[ASN][1000 genomes]
rs10874428	0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs11163898	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[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];0.95[ASN][1000 genomes]
rs11163903	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163905	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163906	0.88[ASW][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs11163907	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163908	0.80[AMR][1000 genomes]
rs12057561	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs12064926	0.80[AMR][1000 genomes]
rs12070547	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094426	0.80[AMR][1000 genomes]
rs12119275	0.81[CHD][hapmap]
rs12132032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565896	0.83[MEX][hapmap]
rs12723299	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs12724598	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12746741	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12748859	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs12759624	0.80[AMR][1000 genomes]
rs12760594	0.80[AMR][1000 genomes]
rs1402694	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs1472243	0.82[AMR][1000 genomes]
rs1521518	0.88[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs1565823	0.81[GIH][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs1874070	0.84[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs2037454	0.81[GIH][hapmap]
rs2134646	0.83[MEX][hapmap]
rs2134647	0.83[MEX][hapmap]
rs2134648	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs34179759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34495740	0.95[ASN][1000 genomes]
rs35452337	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3861699	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6576960	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs6576962	0.88[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs6576963	0.83[MEX][hapmap]
rs6661492	0.80[AMR][1000 genomes]
rs6669045	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6695305	0.80[AMR][1000 genomes]
rs6696125	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs6703653	0.84[JPT][hapmap]
rs67276144	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72711192	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7512288	0.80[AMR][1000 genomes]
rs7515264	0.80[AMR][1000 genomes]
rs7515976	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs7520283	0.84[JPT][hapmap]
rs7532712	0.80[AMR][1000 genomes]
rs903263	0.83[MEX][hapmap]
rs953197	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs970318	0.81[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12404263	MCOLN2	cis	parietal	SCAN
rs12404263	PRKACB	cis	lymphoblastoid	seeQTL
rs12404263	BCL10	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84544600-84556200	Weak transcription	Pancreas	Pancrea
2	chr1:84544600-84557200	Weak transcription	Gastric	stomach
3	chr1:84544800-84551800	Weak transcription	Spleen	Spleen
4	chr1:84544800-84556000	Weak transcription	Primary T cells from cord blood	blood
5	chr1:84544800-84556200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:84545000-84551800	Weak transcription	Right Ventricle	heart
7	chr1:84545000-84553400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:84545000-84554200	Weak transcription	HSMM	muscle
9	chr1:84545000-84554400	Weak transcription	A549	lung
10	chr1:84545000-84554600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:84545000-84554800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:84545000-84554800	Weak transcription	HSMMtube	muscle
13	chr1:84545000-84556200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:84545000-84557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:84545000-84558800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:84545000-84560600	Weak transcription	Fetal Lung	lung
17	chr1:84545000-84561200	Weak transcription	Ovary	ovary
18	chr1:84545000-84566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:84545200-84554600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:84545200-84554800	Weak transcription	NHEK	skin
22	chr1:84545200-84555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:84545400-84556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:84545400-84560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:84545800-84552800	Weak transcription	Brain Germinal Matrix	brain
27	chr1:84545800-84553600	Weak transcription	Fetal Heart	heart
28	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:84546000-84554400	Weak transcription	Hela-S3	cervix
30	chr1:84546400-84555000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:84546400-84560400	Weak transcription	Dnd41	blood
32	chr1:84549000-84554200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:84549200-84555000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:84549400-84553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:84549800-84554600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:84549800-84555000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:84550000-84554600	Weak transcription	Brain Substantia Nigra	brain
38	chr1:84551200-84552200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:84551400-84552000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:84551400-84552000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:84551400-84552000	Strong transcription	Fetal Intestine Large	intestine
42	chr1:84551400-84552200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:84551400-84552200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:84551400-84552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:84551400-84552200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:84551400-84552200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:84551400-84552400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:84551400-84552600	Strong transcription	Fetal Intestine Small	intestine
49	chr1:84551400-84552600	Strong transcription	Fetal Stomach	stomach
50	chr1:84551600-84551800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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