Variant report

Variant	rs12134359
Chromosome Location	chr1:94203051-94203052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94144900..94147325-chr1:94201561..94203406,2	MCF-7	breast:
2	chr1:94194863..94197448-chr1:94201555..94203436,2	K562	blood:
3	chr1:94199457..94202418-chr1:94202668..94205651,2	K562	blood:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10489602	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10489604	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs10782966	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782967	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11165020	0.88[EUR][1000 genomes]
rs11165024	0.85[EUR][1000 genomes]
rs12027630	0.83[EUR][1000 genomes]
rs12122113	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12123957	0.84[EUR][1000 genomes]
rs12137687	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140446	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12143274	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12143279	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563731	0.85[EUR][1000 genomes]
rs12565614	0.87[EUR][1000 genomes]
rs12566531	0.85[EUR][1000 genomes]
rs12734571	0.83[EUR][1000 genomes]
rs12739186	0.87[EUR][1000 genomes]
rs12745990	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884018	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2143990	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235971	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2391315	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs2747039	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747041	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747043	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2747045	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747046	1.00[YRI][hapmap]
rs2747050	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2818160	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818162	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818164	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818169	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3000471	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747965	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs4075523	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4141736	0.83[EUR][1000 genomes]
rs4141737	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs4240955	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240956	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4314890	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4350209	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4847253	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847256	0.82[CEU][hapmap]
rs4847258	1.00[YRI][hapmap]
rs6664719	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs6685747	0.95[EUR][1000 genomes]
rs7364910	0.87[EUR][1000 genomes]
rs8179391	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs871854	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12134359	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs12134359	RP11-488P3.1	cis	Artery Tibial	GTEx
rs12134359	RP11-488P3.1	cis	Stomach	GTEx
rs12134359	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12134359	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs12134359	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs12134359	RP11-488P3.1	cis	lung	GTEx
rs12134359	RP11-488P3.1	cis	Thyroid	GTEx
rs12134359	RP11-488P3.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94196200-94205800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:94196600-94204000	Weak transcription	Lung	lung
3	chr1:94197600-94205800	Weak transcription	Spleen	Spleen
4	chr1:94197800-94205800	Weak transcription	Right Atrium	heart
5	chr1:94199000-94204000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:94199000-94204000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:94199000-94207000	Enhancers	HSMM	muscle
8	chr1:94199400-94204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:94199400-94205800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:94199400-94217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:94199600-94203200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:94199600-94204800	Enhancers	Osteobl	bone
13	chr1:94200000-94204000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:94200200-94204800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:94200200-94207000	Enhancers	NHDF-Ad	bronchial
16	chr1:94200400-94203800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:94200400-94206000	Enhancers	HMEC	breast
18	chr1:94200600-94203800	Enhancers	NHEK	skin
19	chr1:94200600-94204000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:94200600-94205400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:94200800-94205800	Weak transcription	HepG2	liver
22	chr1:94201000-94203600	Weak transcription	A549	lung
23	chr1:94201000-94203800	Weak transcription	Hela-S3	cervix
24	chr1:94201200-94206200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:94201400-94203200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:94202200-94203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:94202200-94203600	Weak transcription	HSMMtube	muscle
28	chr1:94202200-94205000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:94202600-94206800	Enhancers	NHLF	lung
30	chr1:94202800-94203400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:94203000-94203200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:94203000-94203600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:94203000-94203800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:94203000-94205000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:94203000-94205000	Enhancers	NH-A	brain
36	chr1:94203000-94206800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links