Variant report

Variant	rs10878109
Chromosome Location	chr12:64543190-64543191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10784382	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784383	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175267	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs2669626	0.81[EUR][1000 genomes]
rs71278252	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131691	0.81[CEU][hapmap]
rs7964633	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7965130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64531600-64554400	Weak transcription	NH-A	brain
2	chr12:64537000-64545600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:64537200-64546400	Weak transcription	Stomach Mucosa	stomach
4	chr12:64537400-64544600	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:64537600-64543600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:64537800-64543200	Weak transcription	Ovary	ovary
7	chr12:64537800-64547600	Weak transcription	Hela-S3	cervix
8	chr12:64537800-64551000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:64538000-64544800	Weak transcription	Adipose Nuclei	Adipose
10	chr12:64538000-64545000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:64538000-64553400	Weak transcription	HMEC	breast
12	chr12:64539400-64544600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:64539600-64544800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:64539600-64544800	Weak transcription	Fetal Stomach	stomach
15	chr12:64540000-64553400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:64540000-64553400	Weak transcription	NHEK	skin
17	chr12:64540400-64553400	Weak transcription	Osteobl	bone
18	chr12:64540400-64553800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:64540400-64558800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:64540600-64546000	Weak transcription	Fetal Brain Female	brain
21	chr12:64541400-64543800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:64541400-64545200	Weak transcription	Lung	lung
23	chr12:64541400-64545600	Weak transcription	Fetal Brain Male	brain
24	chr12:64541400-64550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:64541400-64554400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:64541600-64543600	Strong transcription	A549	lung
27	chr12:64541800-64543600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:64542000-64543200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:64542400-64543200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:64542400-64546400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:64542400-64553800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:64542600-64543200	Strong transcription	NHDF-Ad	bronchial
33	chr12:64542600-64543400	Strong transcription	HSMMtube	muscle
34	chr12:64542600-64543800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:64542600-64544200	Strong transcription	NHLF	lung
36	chr12:64542600-64544400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:64542800-64543600	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links