Variant report

Variant	rs12352643
Chromosome Location	chr9:101157125-101157126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101136620..101139249-chr9:101156990..101158557,2	K562	blood:
2	chr9:101156357..101157918-chr9:101159602..101161202,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10115570	1.00[CEU][hapmap]
rs10118761	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10120040	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10120099	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10122943	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs10429522	0.93[GIH][hapmap]
rs10760298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818832	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818833	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818857	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10818863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818876	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818896	0.86[GIH][hapmap]
rs10986060	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10986084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs10986125	0.92[GIH][hapmap]
rs12340823	0.93[CEU][hapmap]
rs12352641	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];1.00[ASN][1000 genomes]
rs16915331	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs16915442	0.89[CHD][hapmap]
rs16915579	0.89[CHD][hapmap]
rs17696686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17768880	0.90[CEU][hapmap]
rs2304388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3780421	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56281459	0.87[ASN][1000 genomes]
rs57298260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029062	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7031472	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7032844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041599	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7042831	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7044824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7044961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045221	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7046871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724890	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9886725	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs9886874	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3356278	chr9:101153231-101157729	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12352643	GALNT12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101128200-101164200	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101144000-101172000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:101149800-101158600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:101150400-101157800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:101155000-101157800	Weak transcription	Primary B cells from cord blood	blood
6	chr9:101155000-101157800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:101156400-101159600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:101156600-101172000	Weak transcription	Fetal Brain Female	brain

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