Variant report

Variant	rs702373
Chromosome Location	chr10:43422802-43422803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1621595	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17158318	0.86[ASN][1000 genomes]
rs17158320	0.86[ASN][1000 genomes]
rs17158328	0.85[ASN][1000 genomes]
rs1774189	0.82[ASN][1000 genomes]
rs1774198	0.94[ASN][1000 genomes]
rs1774200	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1774201	0.94[ASN][1000 genomes]
rs1775058	0.82[ASN][1000 genomes]
rs1775090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775095	0.83[ASN][1000 genomes]
rs2795523	0.92[ASN][1000 genomes]
rs702374	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs702375	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs734106	0.86[ASN][1000 genomes]
rs788259	0.81[EUR][1000 genomes]
rs788268	0.86[ASN][1000 genomes]
rs788272	0.86[ASN][1000 genomes]
rs788274	0.84[ASN][1000 genomes]
rs788275	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs788277	0.93[ASN][1000 genomes]
rs788278	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs788282	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs947692	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs702373	CSGALNACT2	cis	parietal	SCAN
rs702373	CSGALNACT2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43419800-43423600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr10:43420000-43423000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:43421000-43423000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr10:43421200-43423000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr10:43422200-43423000	Enhancers	Fetal Muscle Leg	muscle
6	chr10:43422200-43423200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr10:43422200-43423200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:43422200-43423200	Bivalent Enhancer	Fetal Stomach	stomach
9	chr10:43422200-43423200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr10:43422200-43423600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:43422400-43423000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr10:43422400-43423200	Enhancers	Fetal Lung	lung
13	chr10:43422600-43423000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr10:43422600-43423000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:43422600-43423200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr10:43422800-43423000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr10:43422800-43423200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:43422800-43423600	Enhancers	Adipose Nuclei	Adipose
19	chr10:43422800-43425400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr10:43422800-43428200	Weak transcription	Pancreas	Pancrea

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