Variant report

Variant	rs12142643
Chromosome Location	chr1:76603648-76603649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11162086	0.81[JPT][hapmap]
rs12140157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs289697	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs3011996	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs3843263	0.81[JPT][hapmap]
rs901490	0.81[JPT][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	nsv1488	chr1:76587622-76632635	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12142643	TRAM1	trans	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76576600-76620000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76588200-76615600	Weak transcription	Left Ventricle	heart
5	chr1:76591200-76607800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:76592600-76610800	Weak transcription	Fetal Kidney	kidney
7	chr1:76592800-76605800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:76593000-76608200	Weak transcription	Fetal Lung	lung
9	chr1:76594200-76607400	Weak transcription	Fetal Brain Female	brain
10	chr1:76594600-76615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:76598600-76609800	Weak transcription	Fetal Stomach	stomach
12	chr1:76599800-76620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:76601200-76604600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:76601400-76603800	Enhancers	Brain Anterior Caudate	brain
15	chr1:76601400-76604000	Enhancers	Brain Substantia Nigra	brain
16	chr1:76601600-76605200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:76601800-76605600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:76601800-76606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:76601800-76608200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:76602000-76607600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:76602800-76604600	Enhancers	Adipose Nuclei	Adipose
22	chr1:76603000-76605200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:76603000-76605600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:76603400-76604400	Enhancers	HUVEC	blood vessel
25	chr1:76603600-76604000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:76603600-76604400	Enhancers	Stomach Mucosa	stomach
27	chr1:76603600-76604800	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:76603600-76608000	Weak transcription	Right Atrium	heart

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