Variant report

Variant	rs9892037
Chromosome Location	chr17:34003880-34003881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12103729	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150473	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150480	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321597	0.82[CHB][hapmap]
rs321600	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs321602	0.83[EUR][1000 genomes]
rs34619890	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4516277	0.82[CHB][hapmap]
rs55898431	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56056154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56227129	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56292300	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61515677	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72828056	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72828059	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72828073	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72828093	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs740913	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9892539	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904187	0.94[CEU][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9906309	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9906872	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908809	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909815	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9911836	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs9892037	TBC1D29	cis	parietal	SCAN
rs9892037	PEX12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr17:33954600-34006000	Weak transcription	Stomach Mucosa	stomach
5	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr17:33977200-34010400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:33979400-34016600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:33982000-34007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:33992800-34028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:33994600-34004400	Strong transcription	A549	lung
13	chr17:33994800-34010600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:33995000-34007000	Weak transcription	Fetal Intestine Small	intestine
15	chr17:33995400-34004200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:33995800-34004000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:33995800-34024600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:33996000-34010800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr17:33996400-34004000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:33996400-34005800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:33997000-34010400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:33997400-34023200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:33997600-34004200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr17:33997600-34024600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:33998000-34006400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:33999000-34008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
28	chr17:33999600-34008400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr17:33999600-34018200	Weak transcription	Fetal Kidney	kidney
30	chr17:33999800-34010600	Weak transcription	Psoas Muscle	Psoas
31	chr17:34000000-34014200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr17:34001200-34004400	Strong transcription	NHEK	skin
33	chr17:34001400-34007400	Weak transcription	Brain Hippocampus Middle	brain
34	chr17:34001600-34004600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:34001600-34006800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:34001800-34004800	Weak transcription	Fetal Stomach	stomach
37	chr17:34001800-34006200	Weak transcription	Fetal Muscle Leg	muscle
38	chr17:34001800-34007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:34001800-34007400	Weak transcription	Pancreas	Pancrea
40	chr17:34001800-34008000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr17:34001800-34008400	Weak transcription	Fetal Brain Female	brain
42	chr17:34001800-34008400	Weak transcription	Left Ventricle	heart
43	chr17:34001800-34009000	Weak transcription	Spleen	Spleen
44	chr17:34001800-34009600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:34001800-34009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:34001800-34009600	Weak transcription	Aorta	Aorta
47	chr17:34001800-34009600	Weak transcription	Gastric	stomach
48	chr17:34001800-34010800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr17:34001800-34014000	Weak transcription	Right Ventricle	heart
50	chr17:34001800-34014800	Weak transcription	Brain Substantia Nigra	brain

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