Variant report

Variant	rs10493578
Chromosome Location	chr1:76490234-76490235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493580	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11162070	0.92[EUR][1000 genomes]
rs11162073	0.90[EUR][1000 genomes]
rs11805321	0.88[EUR][1000 genomes]
rs12023970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12035171	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038667	0.86[EUR][1000 genomes]
rs12039427	0.88[EUR][1000 genomes]
rs12040748	0.88[EUR][1000 genomes]
rs12045798	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1344929	0.86[ASN][1000 genomes]
rs2289240	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2289241	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4083965	1.00[JPT][hapmap]
rs4146895	0.85[EUR][1000 genomes]
rs4146896	0.85[EUR][1000 genomes]
rs4949690	0.88[EUR][1000 genomes]
rs58483436	0.82[EUR][1000 genomes]
rs59862803	0.86[ASN][1000 genomes]
rs6686341	1.00[JPT][hapmap]
rs6688802	1.00[JPT][hapmap]
rs6703050	1.00[JPT][hapmap]
rs6703053	1.00[JPT][hapmap]
rs6703146	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6704184	0.86[EUR][1000 genomes]
rs7513692	1.00[JPT][hapmap]
rs7517793	0.88[EUR][1000 genomes]
rs7517974	0.88[EUR][1000 genomes]
rs7529565	0.91[EUR][1000 genomes]
rs7550814	1.00[JPT][hapmap]
rs7556623	0.83[AMR][1000 genomes];0.95[EUR][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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10493578	ACADM	cis	cerebellum	SCAN
rs10493578	MSH4	cis	cerebellum	SCAN
rs10493578	LRRIQ3	cis	cerebellum	SCAN
rs10493578	MSH4	cis	parietal	SCAN
rs10493578	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76487400-76491000	Enhancers	Fetal Lung	lung
2	chr1:76488200-76491800	Enhancers	Primary T cells from cord blood	blood
3	chr1:76488400-76490400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:76488600-76490400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:76488800-76490600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:76489000-76490400	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:76489000-76490600	Enhancers	NHEK	skin
8	chr1:76489200-76490400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:76489200-76490600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:76489200-76490600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:76489200-76490800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:76489200-76490800	Enhancers	HMEC	breast
13	chr1:76489400-76490600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:76489400-76490800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:76489400-76490800	Enhancers	Fetal Heart	heart
16	chr1:76489600-76490400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:76489600-76490400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:76489600-76490400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:76489600-76490400	Enhancers	NH-A	brain
20	chr1:76489600-76491200	Enhancers	Fetal Stomach	stomach
21	chr1:76489800-76490400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:76489800-76490600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:76489800-76491000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:76489800-76491000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:76489800-76502800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:76490200-76490600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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