Variant report

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10485912	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs1207870	0.81[YRI][hapmap]
rs1207882	0.81[YRI][hapmap]
rs186533	0.88[CEU][hapmap]
rs321997	0.84[CEU][hapmap]
rs321999	0.84[CEU][hapmap]
rs322001	0.82[CEU][hapmap]
rs322002	0.88[CEU][hapmap]
rs322004	0.87[CEU][hapmap]
rs323133	0.88[CEU][hapmap]
rs323136	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs323139	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs323149	0.84[CEU][hapmap]
rs323161	0.81[CEU][hapmap]
rs323162	0.90[CEU][hapmap]
rs323163	0.87[CEU][hapmap]
rs323165	0.82[CEU][hapmap]
rs323167	0.88[CEU][hapmap]
rs323169	0.88[CEU][hapmap]
rs323170	0.87[CEU][hapmap]
rs323171	0.87[CEU][hapmap]
rs323174	0.88[CEU][hapmap]
rs73150753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7805425	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1019355	chr7:78319575-78399845	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv607657	chr7:78329795-78483211	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12665877	SEMA3C	cis	cerebellum	SCAN
rs12665877	PRSS53	trans	parietal	SCAN
rs12665877	WBSCR16	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78341200-78346800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:78341400-78344600	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr7:78341400-78345400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:78341800-78344800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:78342200-78346000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:78343000-78344600	Enhancers	Brain Cingulate Gyrus	brain
7	chr7:78343200-78344600	Enhancers	Fetal Brain Male	brain
8	chr7:78343600-78346600	Weak transcription	Pancreas	Pancrea
9	chr7:78343600-78347600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:78343800-78344600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr7:78343800-78344600	Enhancers	Brain Hippocampus Middle	brain
12	chr7:78344000-78345200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr7:78344000-78346000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:78344200-78344800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:78344200-78346200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:78344400-78346200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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