Variant report

Variant	rs10986084
Chromosome Location	chr9:101147503-101147504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101146357..101148869-chr9:101551547..101553661,2	K562	blood:
2	chr9:101142401..101145561-chr9:101146082..101148768,4	K562	blood:
3	chr9:101134634..101137375-chr9:101146278..101148960,2	K562	blood:
4	chr9:101146313..101147823-chr9:101149379..101151101,2	K562	blood:

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10115570	1.00[CEU][hapmap]
rs10118761	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10120040	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10120099	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10122943	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs10760298	0.95[ASN][1000 genomes]
rs10818832	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818833	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818857	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10818863	0.95[ASN][1000 genomes]
rs10818876	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10986060	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10986071	0.82[JPT][hapmap]
rs10986073	0.85[JPT][hapmap]
rs10986076	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10986078	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10986080	0.85[EUR][1000 genomes]
rs10986085	0.84[AFR][1000 genomes]
rs12006182	0.94[YRI][hapmap]
rs12340823	0.93[CEU][hapmap]
rs12344879	0.83[EUR][1000 genomes]
rs12346403	0.86[EUR][1000 genomes]
rs12352641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs12352643	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]
rs16915331	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs16915442	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs16915579	0.89[CHD][hapmap]
rs17696686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs17768880	0.90[CEU][hapmap]
rs2304388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs3205936	0.95[YRI][hapmap]
rs3780421	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs55739315	0.80[AFR][1000 genomes]
rs56281459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56326520	0.80[AFR][1000 genomes]
rs57298260	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57686796	0.82[EUR][1000 genomes]
rs59263286	0.80[AFR][1000 genomes]
rs62574569	0.86[EUR][1000 genomes]
rs62576564	0.82[EUR][1000 genomes]
rs6478702	0.90[YRI][hapmap]
rs7025048	0.95[YRI][hapmap]
rs7029062	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7031472	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7032844	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]
rs7041599	0.95[ASN][1000 genomes]
rs7042831	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs7044824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7044963	0.90[YRI][hapmap]
rs7045221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7046871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs7047634	0.85[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs724890	1.00[CEU][hapmap];0.97[ASN][1000 genomes]
rs73497003	0.84[AFR][1000 genomes]
rs73497005	0.80[AFR][1000 genomes]
rs73497010	0.80[AFR][1000 genomes]
rs73655418	0.80[AFR][1000 genomes]
rs9886725	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs9886874	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10986084	GALNT12	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101128200-101164200	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101129000-101156000	Weak transcription	Fetal Brain Female	brain
3	chr9:101143200-101148600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:101143200-101156000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:101143200-101157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:101143400-101148800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:101144000-101172000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:101144400-101152800	Weak transcription	Brain Angular Gyrus	brain
9	chr9:101144600-101147600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:101144600-101147600	Weak transcription	GM12878-XiMat	blood
11	chr9:101145000-101147600	Weak transcription	Primary B cells from cord blood	blood
12	chr9:101147400-101148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:101147400-101148600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:101147400-101152000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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