Variant report

Variant	rs9906872
Chromosome Location	chr17:33996764-33996765
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	chr17:33996336..33998248-chr17:34000233..34002749,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12103451	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12103729	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150473	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150480	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971277	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321597	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs321600	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs321602	0.82[EUR][1000 genomes]
rs34619890	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4516277	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs55898431	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56056154	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56227129	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56292300	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61515677	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72828056	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72828059	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72828073	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828084	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72828093	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs740913	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9892037	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9892539	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904187	0.94[CEU][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9906309	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908809	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909815	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9911836	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9906872	TBC1D29	cis	parietal	SCAN
rs9906872	PEX12	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
5	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:33949200-34001200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:33954600-34001800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:33954600-34006000	Weak transcription	Stomach Mucosa	stomach
9	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:33963400-34001200	Weak transcription	Aorta	Aorta
11	chr17:33966000-34002000	Strong transcription	Primary T cells from cord blood	blood
12	chr17:33968000-33997600	Weak transcription	HSMMtube	muscle
13	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:33968400-33997800	Weak transcription	Brain Substantia Nigra	brain
15	chr17:33969000-34001200	Weak transcription	Right Ventricle	heart
16	chr17:33969400-34001200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr17:33969600-33997600	Weak transcription	Brain Anterior Caudate	brain
18	chr17:33969600-33998600	Weak transcription	Fetal Brain Male	brain
19	chr17:33970000-33997800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:33970400-34001200	Weak transcription	Small Intestine	intestine
21	chr17:33971200-33997800	Weak transcription	Colon Smooth Muscle	Colon
22	chr17:33972000-33998800	Weak transcription	Ovary	ovary
23	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:33977200-34010400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:33977800-33997800	Weak transcription	Gastric	stomach
26	chr17:33978000-33997800	Weak transcription	Lung	lung
27	chr17:33978000-34001200	Weak transcription	Brain Angular Gyrus	brain
28	chr17:33978200-33997800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr17:33978200-33997800	Weak transcription	Fetal Brain Female	brain
30	chr17:33979400-34016600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:33980800-33998200	Weak transcription	Brain Germinal Matrix	brain
32	chr17:33981400-33997800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:33981400-34001200	Weak transcription	Pancreas	Pancrea
34	chr17:33981600-33997800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr17:33982000-34007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr17:33985000-33996800	Weak transcription	NHDF-Ad	bronchial
37	chr17:33985000-33997600	Weak transcription	NHLF	lung
38	chr17:33985000-33998800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:33985000-33999200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr17:33985400-34001200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:33985800-33997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:33985800-33998600	Weak transcription	Fetal Kidney	kidney
43	chr17:33987400-33996800	Weak transcription	Colonic Mucosa	Colon
44	chr17:33987400-33997800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:33987400-33997800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr17:33987400-33997800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr17:33988400-33997800	Weak transcription	Fetal Heart	heart
48	chr17:33988600-33998200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:33988600-34002400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr17:33989600-33999000	Weak transcription	Hela-S3	cervix

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