Variant report

Variant	rs9886725
Chromosome Location	chr9:101140313-101140314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101138177..101140761-chr9:101153735..101155417,2	K562	blood:
2	chr9:101125220..101129376-chr9:101135603..101141784,6	K562	blood:
3	chr9:101076714..101079334-chr9:101138741..101140975,3	K562	blood:
4	chr9:101076603..101078214-chr9:101139182..101140975,2	K562	blood:
5	chr9:101135605..101137145-chr9:101138879..101140848,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10115570	1.00[CEU][hapmap]
rs10122943	1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs10818832	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818833	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10818876	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10986060	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10986076	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10986078	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10986080	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10986084	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs10986125	1.00[CHD][hapmap]
rs12340823	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs12344879	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12346403	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12352641	1.00[CEU][hapmap]
rs12352643	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs16915331	0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs17696686	1.00[CEU][hapmap]
rs17768880	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs2304388	1.00[CEU][hapmap]
rs3780421	1.00[CEU][hapmap]
rs56281459	0.82[EUR][1000 genomes]
rs57686796	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583641	1.00[CHD][hapmap]
rs62574569	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576560	0.91[EUR][1000 genomes]
rs62576561	0.91[EUR][1000 genomes]
rs62576562	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62576564	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029062	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs7031472	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7032844	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7041599	0.81[AMR][1000 genomes]
rs7042831	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7044824	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7044961	1.00[CEU][hapmap]
rs7045221	0.80[EUR][1000 genomes]
rs7046871	1.00[CEU][hapmap]
rs724890	1.00[CEU][hapmap]
rs9886874	0.93[CEU][hapmap];0.92[EUR][1000 genomes]

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
rs9886725	GALNT12	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101126600-101142600	Weak transcription	Brain Angular Gyrus	brain
2	chr9:101128200-101164200	Weak transcription	Brain Germinal Matrix	brain
3	chr9:101129000-101156000	Weak transcription	Fetal Brain Female	brain
4	chr9:101132800-101142800	Weak transcription	Right Atrium	heart
5	chr9:101133400-101142400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:101134200-101142600	Enhancers	Fetal Intestine Large	intestine
7	chr9:101134400-101142400	Enhancers	Fetal Intestine Small	intestine
8	chr9:101134800-101142400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:101134800-101143000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:101136800-101144600	Enhancers	Primary B cells from peripheral blood	blood
11	chr9:101137000-101145000	Enhancers	Primary B cells from cord blood	blood
12	chr9:101137400-101142200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:101137400-101142200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:101137400-101142400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:101137600-101142200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:101137600-101142200	Weak transcription	Fetal Heart	heart
17	chr9:101137600-101142400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:101137600-101142400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:101137800-101142200	Weak transcription	A549	lung
20	chr9:101137800-101142400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:101137800-101142400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:101137800-101142400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:101137800-101142400	Weak transcription	HMEC	breast
24	chr9:101137800-101142400	Weak transcription	HSMM	muscle
25	chr9:101137800-101142400	Weak transcription	HSMMtube	muscle
26	chr9:101138000-101140600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:101138000-101140600	Weak transcription	NHLF	lung
28	chr9:101138000-101142400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:101138000-101142400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:101138000-101142600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:101138200-101140400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:101138200-101140600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:101138200-101140600	Weak transcription	NH-A	brain
34	chr9:101138200-101142200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:101138200-101142200	Weak transcription	HUVEC	blood vessel
36	chr9:101138200-101142400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:101138400-101142400	Weak transcription	GM12878-XiMat	blood
38	chr9:101138400-101142600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:101139400-101140600	Weak transcription	K562	blood
40	chr9:101140000-101140800	Enhancers	Fetal Muscle Trunk	muscle
41	chr9:101140000-101141400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:101140000-101141600	Enhancers	NHDF-Ad	bronchial
43	chr9:101140200-101141000	Enhancers	Placenta	Placenta
44	chr9:101140200-101141200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:101140200-101141800	Enhancers	Osteobl	bone
46	chr9:101140200-101142400	Weak transcription	Pancreas	Pancrea
47	chr9:101140200-101142400	Weak transcription	Spleen	Spleen

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