Variant report

Variant	rs1316508
Chromosome Location	chr1:210710747-210710748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11119529	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119531	0.83[ASN][1000 genomes]
rs11119532	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490222	0.96[YRI][hapmap]
rs2501911	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs4132902	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs4844531	0.88[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7514187	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv549106	chr1:210698719-210736508	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1011702	chr1:210706323-210739030	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv988198	chr1:210707300-210716552	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1316508	LGTN	cis	cerebellum	SCAN
rs1316508	PIGR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210674400-210719600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210680600-210731000	Weak transcription	HSMM	muscle
3	chr1:210708200-210711000	Enhancers	HSMMtube	muscle
4	chr1:210709200-210710800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:210709400-210715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:210709600-210710800	Enhancers	Brain Hippocampus Middle	brain
7	chr1:210709800-210710800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:210709800-210711000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr1:210709800-210715200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:210710000-210715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:210710000-210715000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:210710000-210715000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:210710000-210715200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:210710000-210715200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:210710000-210715400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:210710200-210715200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:210710200-210715200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:210710200-210715200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:210710400-210715200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:210710600-210715200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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