Variant report

Variant	rs12344631
Chromosome Location	chr9:103907209-103907210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10113988	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs10117175	0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs10121939	0.88[JPT][hapmap];0.86[AMR][1000 genomes]
rs10156478	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10989422	0.86[AMR][1000 genomes]
rs10989423	0.85[AMR][1000 genomes]
rs10989424	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs10989425	0.87[AMR][1000 genomes]
rs10989426	0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs12336617	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs12336728	0.86[AMR][1000 genomes]
rs12338716	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs12339921	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs12339994	0.86[AMR][1000 genomes]
rs12342841	0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs12345075	0.85[AMR][1000 genomes]
rs12345440	0.85[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs12346158	0.85[AMR][1000 genomes]
rs12346223	0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs12346256	0.83[JPT][hapmap];0.85[AMR][1000 genomes]
rs12347855	0.86[AMR][1000 genomes]
rs12349128	0.86[AMR][1000 genomes]
rs12350583	0.85[AMR][1000 genomes]
rs12351067	0.81[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs12352151	0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs12353249	0.86[AMR][1000 genomes]
rs12685239	0.85[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs12686592	0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs1410854	0.81[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1431476	0.81[JPT][hapmap]
rs1431477	0.90[MEX][hapmap];0.83[AMR][1000 genomes]
rs16920038	0.86[AMR][1000 genomes]
rs16920055	0.83[AMR][1000 genomes]
rs2116285	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs2303980	0.85[JPT][hapmap]
rs2987735	0.85[JPT][hapmap]
rs57056311	0.86[AMR][1000 genomes]
rs58661374	0.85[AMR][1000 genomes]
rs61342570	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61654883	0.85[AMR][1000 genomes]
rs67133619	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7029916	0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs735847	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs9697078	0.82[JPT][hapmap]

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	nsv831671	chr9:103858107-104020816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv948791	chr9:103893030-103964650	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv466443	chr9:103895161-103923185	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv614961	chr9:103895161-103923185	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12344631	ZNF367	cis	cerebellum	SCAN
rs12344631	NR4A3	cis	parietal	SCAN
rs12344631	LPPR1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103904400-103909000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:103904800-103909000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:103905200-103909800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:103905200-103910000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:103905200-103910200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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