Variant report

Variant	rs491554
Chromosome Location	chr7:140776614-140776615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140776160..140778796-chr7:140827028..140829508,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11762357	0.93[ASN][1000 genomes]
rs1860752	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2365575	0.89[ASN][1000 genomes]
rs4726263	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498933	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511001	1.00[ASN][1000 genomes]
rs534348	1.00[ASN][1000 genomes]
rs536809	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553046	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55949610	0.94[ASN][1000 genomes]
rs560981	0.94[ASN][1000 genomes]
rs6464278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6464330	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs6944492	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960603	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6962233	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6967482	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs722219	0.94[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7778658	0.92[ASN][1000 genomes]
rs7805034	0.94[ASN][1000 genomes]
rs7806026	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7810146	0.89[ASN][1000 genomes]
rs7810541	0.91[CEU][hapmap]
rs801157	1.00[ASN][1000 genomes]
rs801158	1.00[ASN][1000 genomes]
rs9640323	0.94[ASN][1000 genomes]
rs9886312	0.91[CEU][hapmap];0.82[CHD][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889248	chr7:140754785-140809205	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3417140	chr7:140768130-140783190	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs491554	ADCK2	cis	cerebellum	SCAN
rs491554	AK096481	cis	multi-tissue	Pritchard
rs491554	TMEM178B	cis	Esophagus Mucosa	GTEx
rs491554	OR6B1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140770600-140777000	Active TSS	Fetal Brain Female	brain
2	chr7:140770800-140776800	Active TSS	Brain Cingulate Gyrus	brain
3	chr7:140771000-140777000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr7:140771000-140777000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:140772000-140777000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:140774400-140776800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr7:140774800-140776800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:140774800-140783200	Weak transcription	Pancreas	Pancrea
9	chr7:140775600-140776800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:140776000-140776800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:140776000-140777000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr7:140776000-140778600	Active TSS	Brain Anterior Caudate	brain
13	chr7:140776200-140776800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:140776200-140776800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr7:140776200-140776800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr7:140776200-140776800	Enhancers	Psoas Muscle	Psoas
17	chr7:140776200-140777000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:140776600-140776800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr7:140776600-140776800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:140776600-140776800	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr7:140776600-140776800	Flanking Active TSS	Fetal Brain Male	brain
22	chr7:140776600-140777200	Flanking Active TSS	Brain Germinal Matrix	brain

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