Variant report

Variant	rs12685966
Chromosome Location	chr9:8313681-8313682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10511493	0.93[CEU][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs10758952	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10815822	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10976953	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10976960	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10976962	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11521513	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11521514	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11524180	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12551994	0.86[EUR][1000 genomes]
rs12554953	0.86[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap]
rs12555185	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12555436	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12682697	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12682993	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12684196	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12684395	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12684864	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16927547	0.93[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs20514	0.93[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap]
rs2173711	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739578	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3739579	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3780336	0.93[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3847288	0.93[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs3847291	0.93[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4008212	0.81[AMR][1000 genomes]
rs4008216	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4742486	0.90[CEU][hapmap]
rs7042854	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72710309	0.91[EUR][1000 genomes]
rs7848455	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7848705	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7848818	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs7854665	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7873084	0.93[CEU][hapmap];0.84[JPT][hapmap]

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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv892223	chr9:8258921-8318948	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	miRNA target site	n/a	inside rSNPs	diseases
4	nsv892224	chr9:8263737-8338431	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	miRNA target site	n/a	inside rSNPs	diseases
5	esv3337718	chr9:8301001-8318939	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12685966	KIAA2026	cis	cerebellum	SCAN
rs12685966	FIG4	trans	parietal	SCAN
rs12685966	ZNF785	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8309200-8315600	Weak transcription	Fetal Kidney	kidney
2	chr9:8310800-8318600	Weak transcription	Fetal Brain Male	brain
3	chr9:8310800-8321800	Weak transcription	Fetal Brain Female	brain
4	chr9:8310800-8323000	Weak transcription	Brain Germinal Matrix	brain
5	chr9:8311000-8319600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:8311200-8315200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:8311200-8318600	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:8311200-8322600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:8312200-8322600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:8312200-8338200	Weak transcription	Brain Angular Gyrus	brain
11	chr9:8312800-8314600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:8312800-8322000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:8313000-8313800	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr9:8313200-8314400	Strong transcription	Fetal Lung	lung
15	chr9:8313600-8314600	Weak transcription	Brain Substantia Nigra	brain

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