Variant report

Variant	rs707444
Chromosome Location	chr1:72949290-72949291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493499	1.00[ASN][1000 genomes]
rs11586991	0.93[ASN][1000 genomes]
rs11588862	0.87[ASN][1000 genomes]
rs11589261	0.87[ASN][1000 genomes]
rs1373914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664411	0.84[AFR][1000 genomes]
rs2590943	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545290	1.00[ASN][1000 genomes]
rs61771778	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61771794	1.00[ASN][1000 genomes]
rs61771795	0.93[ASN][1000 genomes]
rs61771796	0.87[ASN][1000 genomes]
rs61771797	0.87[ASN][1000 genomes]
rs61771798	0.87[ASN][1000 genomes]
rs61771799	0.87[ASN][1000 genomes]
rs72684685	0.87[ASN][1000 genomes]
rs782211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782240	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782242	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782245	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782257	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992956	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422432	chr1:72821856-73148651	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv871873	chr1:72861847-72975877	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv870463	chr1:72861847-72995398	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv871758	chr1:72861847-72995398	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv830215	chr1:72869049-73029787	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs707444	RP11-292O17.1	cis	Esophagus Muscularis	GTEx
rs707444	ST6GALNAC3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72947000-72950000	Enhancers	Thymus	Thymus
2	chr1:72947200-72950000	Enhancers	Dnd41	blood
3	chr1:72948400-72949800	Enhancers	Primary T cells from cord blood	blood
4	chr1:72948600-72949400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:72948600-72949400	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr1:72948600-72950000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:72948600-72950600	Enhancers	HepG2	liver
8	chr1:72948800-72949800	Weak transcription	Fetal Lung	lung
9	chr1:72948800-72949800	Weak transcription	Fetal Thymus	thymus
10	chr1:72948800-72950400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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