Variant report

Variant	rs321999
Chromosome Location	chr7:78323029-78323030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12665877	0.84[CEU][hapmap]
rs178745	0.94[EUR][1000 genomes]
rs186533	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2190663	0.81[CEU][hapmap]
rs2627542	0.94[EUR][1000 genomes]
rs321997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322001	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs322002	0.96[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs322003	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs322004	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs323133	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs323134	0.93[EUR][1000 genomes]
rs323136	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs323139	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs323149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs323157	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs323158	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs323161	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs323162	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs323163	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs323165	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs323167	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs323168	0.90[EUR][1000 genomes]
rs323169	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs323170	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs323171	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs323173	0.94[EUR][1000 genomes]
rs323174	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs323175	0.94[EUR][1000 genomes]
rs323176	0.94[EUR][1000 genomes]
rs323177	0.94[EUR][1000 genomes]
rs440900	0.92[EUR][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	nsv888509	chr7:78307944-78327299	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs321999	SEMA3C	cis	cerebellum	SCAN
rs321999	WBSCR16	cis	cerebellum	SCAN
rs321999	CCL26	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78313800-78334200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:78318000-78326800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:78318400-78327400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:78320200-78323200	Enhancers	Brain Germinal Matrix	brain
5	chr7:78321600-78323600	Enhancers	Brain Cingulate Gyrus	brain
6	chr7:78322200-78323200	Enhancers	Brain Angular Gyrus	brain
7	chr7:78322200-78328800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:78323000-78323200	Enhancers	Brain Substantia Nigra	brain

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