Variant report

Variant	rs13379432
Chromosome Location	chr14:77872509-77872510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77840795..77844789-chr14:77870809..77874889,5	MCF-7	breast:
2	chr14:77872277..77875027-chr14:77918456..77921340,3	MCF-7	breast:
3	chr14:77859431..77861552-chr14:77871084..77872888,2	K562	blood:
4	chr14:77872257..77874007-chr14:78173034..78174621,2	MCF-7	breast:
5	chr14:77795091..77797469-chr14:77871259..77873894,2	MCF-7	breast:
6	chr14:77859416..77861552-chr14:77870946..77872888,2	K562	blood:
7	chr14:77785202..77790958-chr14:77870163..77875663,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151445	Chromatin interaction
ENSG00000100583	Chromatin interaction
ENSG00000100601	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000119705	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000100580	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10141317	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10143629	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149037	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1061629	0.87[CHD][hapmap]
rs11159261	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11539461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11623826	0.87[CHD][hapmap]
rs11624314	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11625365	0.87[CHD][hapmap]
rs11844300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12432582	0.91[ASN][1000 genomes]
rs12433120	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12433521	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12434419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12435136	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12435676	0.86[ASN][1000 genomes]
rs17105749	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176781	0.87[CHD][hapmap]
rs17751406	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751412	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17824034	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17824214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17824322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2063997	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091916	0.87[CHD][hapmap]
rs2242619	0.87[CHD][hapmap]
rs28583775	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28590531	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34180883	0.88[ASN][1000 genomes]
rs3742737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3783985	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs4223	0.87[CHD][hapmap]
rs4575469	0.87[CHD][hapmap]
rs4899652	1.00[JPT][hapmap]
rs4899655	0.87[CHD][hapmap]
rs4903578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4903579	1.00[JPT][hapmap]
rs4903580	1.00[JPT][hapmap]
rs4903581	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59010468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574374	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7155063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156032	1.00[CHB][hapmap]
rs7156671	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs8005759	0.87[CHD][hapmap]
rs8007503	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8010520	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8012548	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017215	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8020537	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963283	0.87[CHD][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	nsv1362	chr14:77853202-77898605	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13379432	TMED8	cis	cerebellum	SCAN
rs13379432	ZDHHC22	cis	parietal	SCAN
rs13379432	RBM25	cis	cerebellum	SCAN
rs13379432	ZDHHC22	cis	cerebellum	SCAN
rs13379432	RGS6	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77859600-77886200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:77862600-77872600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:77867600-77875600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:77870800-77872600	Enhancers	Primary hematopoietic stem cells	blood
5	chr14:77872200-77872800	Enhancers	K562	blood
6	chr14:77872200-77873200	Enhancers	Right Atrium	heart
7	chr14:77872200-77873200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr14:77872200-77873800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr14:77872200-77874200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr14:77872200-77874600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr14:77872400-77873400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr14:77872400-77873600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr14:77872400-77874000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr14:77872400-77874200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:77872400-77888600	Weak transcription	Pancreas	Pancrea

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