Variant report

Variant	rs11617530
Chromosome Location	chr13:48464863-48464864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11620507	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1324801	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1324802	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1408618	0.89[ASN][1000 genomes]
rs1555723	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555724	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1924811	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1974040	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2147502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274189	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406690	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs28874956	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4142533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369555	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4606606	0.86[EUR][1000 genomes]
rs4941616	0.88[ASN][1000 genomes]
rs4942712	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942713	0.89[ASN][1000 genomes]
rs4942717	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942718	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55633570	0.81[ASN][1000 genomes]
rs61972224	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187725	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7329550	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7330169	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7337764	0.89[ASN][1000 genomes]
rs7981303	0.87[ASN][1000 genomes]
rs7998090	0.88[ASN][1000 genomes]
rs9526406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526407	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526414	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526416	0.98[ASN][1000 genomes]
rs9534851	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534856	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534857	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534858	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534859	0.88[ASN][1000 genomes]
rs9534860	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534861	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534862	0.89[ASN][1000 genomes]
rs9534863	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534867	0.87[ASN][1000 genomes]
rs9534888	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9534895	0.83[ASN][1000 genomes]
rs9534900	0.81[ASN][1000 genomes]
rs9534944	0.84[JPT][hapmap]
rs9534947	0.83[JPT][hapmap]
rs9562775	0.82[ASN][1000 genomes]
rs9567941	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11617530	ENOX1	cis	cerebellum	SCAN
rs11617530	SUCLA2	cis	cerebellum	SCAN
rs11617530	DLEU1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48453800-48471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose
4	chr13:48461000-48472200	Weak transcription	Spleen	Spleen
5	chr13:48461000-48472400	Weak transcription	Lung	lung
6	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
7	chr13:48463600-48474600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:48463800-48465200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr13:48464000-48465000	Enhancers	Primary T cells from cord blood	blood
10	chr13:48464000-48465200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr13:48464200-48465000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr13:48464200-48465000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:48464400-48465000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:48464400-48465200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr13:48464400-48465200	Enhancers	HMEC	breast
16	chr13:48464600-48465000	Flanking Active TSS	Dnd41	blood
17	chr13:48464600-48465200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr13:48464600-48467400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr13:48464800-48465000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:48464800-48465000	Flanking Active TSS	HSMMtube	muscle
21	chr13:48464800-48465000	Active TSS	NHEK	skin
22	chr13:48464800-48465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr13:48464800-48469800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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