Variant report

Variant	rs1444090
Chromosome Location	chr12:59465715-59465716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10735877	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12423606	0.82[EUR][1000 genomes]
rs1444089	0.87[EUR][1000 genomes]
rs1444098	0.80[EUR][1000 genomes]
rs17122093	0.82[EUR][1000 genomes]
rs17628225	0.82[EUR][1000 genomes]
rs2197333	0.80[EUR][1000 genomes]
rs61934327	0.83[EUR][1000 genomes]
rs61934328	0.83[EUR][1000 genomes]
rs61934330	0.83[EUR][1000 genomes]
rs61934332	0.81[EUR][1000 genomes]
rs61934333	0.82[EUR][1000 genomes]
rs6650225	0.80[EUR][1000 genomes]
rs7134004	0.92[EUR][1000 genomes]
rs907344	0.97[EUR][1000 genomes]
rs978615	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1444090	MARCH9	cis	parietal	SCAN
rs1444090	NDUFA4L2	cis	cerebellum	SCAN
rs1444090	OR6C74	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59454400-59471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59461400-59468800	Weak transcription	Fetal Stomach	stomach
3	chr12:59461400-59469400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:59461800-59469000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:59462200-59466400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:59463200-59465800	Enhancers	Osteobl	bone
7	chr12:59463200-59466000	Enhancers	NH-A	brain
8	chr12:59463400-59465800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:59464400-59469000	Weak transcription	Fetal Kidney	kidney
10	chr12:59464600-59468800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:59464600-59469000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:59464600-59470000	Weak transcription	HMEC	breast
13	chr12:59464800-59466400	Enhancers	HUVEC	blood vessel
14	chr12:59464800-59468600	Weak transcription	Fetal Lung	lung
15	chr12:59464800-59470000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:59464800-59470000	Weak transcription	NHEK	skin
17	chr12:59465200-59470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:59465400-59467200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:59465600-59465800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:59465600-59466200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links