Variant report

Variant	rs2145382
Chromosome Location	chr1:171885229-171885230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10436867	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10737340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579330	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs12025368	0.86[CHB][hapmap]
rs2093183	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2145381	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180746	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520188	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538839	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7547770	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551737	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2145382	FMO9P	cis	cerebellum	SCAN
rs2145382	BRP44	cis	parietal	SCAN
rs2145382	LOC646870	cis	parietal	SCAN
rs2145382	MPZL1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171879800-171908000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171880400-171885600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:171881000-171885400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:171881000-171886800	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:171882000-171889400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:171882400-171886000	Enhancers	NHEK	skin
7	chr1:171883000-171885800	Enhancers	Brain Hippocampus Middle	brain
8	chr1:171883200-171890400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:171883400-171887400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:171883600-171887600	Enhancers	Brain Substantia Nigra	brain
11	chr1:171883800-171885600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:171884200-171885600	Weak transcription	Brain Anterior Caudate	brain
13	chr1:171884200-171903400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:171884400-171885600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:171884400-171886000	Enhancers	Brain Angular Gyrus	brain
16	chr1:171885000-171885800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:171885000-171886200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:171885000-171887200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:171885200-171886800	Enhancers	HSMMtube	muscle

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links