Variant report

Variant	rs288178
Chromosome Location	chr5:107351517-107351518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10067069	0.82[CHB][hapmap]
rs10076369	0.82[CHB][hapmap]
rs1024975	0.82[CHB][hapmap]
rs10434798	0.82[CHB][hapmap]
rs10434799	0.81[CHB][hapmap]
rs10479423	0.81[CHB][hapmap]
rs1108067	0.81[CHB][hapmap]
rs11742139	0.82[CHB][hapmap]
rs11951176	0.81[CHB][hapmap]
rs12332109	0.82[CHB][hapmap]
rs13161819	0.81[CHB][hapmap]
rs13173786	0.82[CHB][hapmap]
rs158179	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs167012	0.95[JPT][hapmap];0.86[LWK][hapmap]
rs172305	0.83[TSI][hapmap]
rs288159	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288160	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288175	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288177	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288179	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871109	0.82[CHB][hapmap]
rs6897064	0.82[CHB][hapmap]
rs7729356	0.82[CHB][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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs288178	MAN2A1	cis	parietal	SCAN
rs288178	PJA2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107319800-107354000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:107327400-107353400	Weak transcription	Aorta	Aorta
3	chr5:107339200-107352400	Weak transcription	Adipose Nuclei	Adipose
4	chr5:107339200-107357400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:107339200-107361200	Weak transcription	Fetal Heart	heart
6	chr5:107339200-107364200	Weak transcription	Left Ventricle	heart
7	chr5:107339600-107364200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:107339600-107373800	Weak transcription	Primary T cells from cord blood	blood
9	chr5:107342600-107355600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:107344000-107364200	Weak transcription	Psoas Muscle	Psoas
11	chr5:107344400-107363800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:107347800-107353800	Weak transcription	Spleen	Spleen
13	chr5:107349800-107351600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:107349800-107351800	Weak transcription	Dnd41	blood
15	chr5:107349800-107353400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:107350200-107351600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:107350600-107353000	Weak transcription	Fetal Intestine Large	intestine
18	chr5:107350600-107353400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:107350800-107356200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:107351400-107351800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:107351400-107355600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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