Variant report

Variant	rs6561610
Chromosome Location	chr13:51638170-51638171
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	chr13:51637970..51639747-chr13:51643912..51646146,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12869642	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12870315	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12870383	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1328358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4605050	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6561609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325888	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7337587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7338712	0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs751539	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs9535562	0.86[CHB][hapmap]
rs9535567	0.81[ASN][1000 genomes]
rs9535573	0.91[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes]
rs9563016	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596435	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6561610	GUCY1B2	cis	Esophagus Mucosa	GTEx
rs6561610	NUDT15	cis	parietal	SCAN
rs6561610	GUCY1B2	cis	multi-tissue	Pritchard
rs6561610	GUCY1B2	cis	Nerve Tibial	GTEx
rs6561610	GUCY1B2	cis	Liver	GTEx
rs6561610	GUCY1B2	cis	Skin Sun Exposed Lower leg	GTEx
rs6561610	AP1G1	trans	multi-tissue	Pritchard
rs6561610	AP1G1	cis	Liver	GTEx
rs6561610	GUCY1B2	cis	lung	GTEx
rs6561610	GUCY1B2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51632600-51639800	Enhancers	Brain Germinal Matrix	brain
2	chr13:51632800-51639200	Weak transcription	Spleen	Spleen
3	chr13:51633200-51639400	Weak transcription	Fetal Muscle Leg	muscle
4	chr13:51633200-51639800	Weak transcription	Fetal Stomach	stomach
5	chr13:51633200-51641000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:51633400-51638800	Weak transcription	Fetal Lung	lung
7	chr13:51633400-51657800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:51633800-51640000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:51633800-51640800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:51634400-51640800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:51636200-51640000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:51636800-51639800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr13:51637000-51641600	Enhancers	Primary hematopoietic stem cells	blood
14	chr13:51637600-51638200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr13:51637600-51638400	Enhancers	Fetal Muscle Trunk	muscle
16	chr13:51637600-51639600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:51637800-51639200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr13:51638000-51638200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:51638000-51638200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:51638000-51638200	Enhancers	Liver	Liver
21	chr13:51638000-51640800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:51638000-51644600	Enhancers	Fetal Brain Male	brain

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