Variant report

Variant	rs9904187
Chromosome Location	chr17:34042468-34042469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr17:34041532-34042569	SK-N-SH	brain:	n/a	chr17:34042364-34042378
2	GATA3	chr17:34041821-34042503	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr17:34041709-34042545	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RPL17P42	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12103451	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12103729	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12150473	0.81[EUR][1000 genomes]
rs12150480	0.81[EUR][1000 genomes]
rs16971277	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34619890	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56056154	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56292300	0.87[EUR][1000 genomes]
rs61515677	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72828084	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72828093	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740913	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9892037	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9892539	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9906309	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9906872	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9909815	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9911836	0.86[AMR][1000 genomes];0.83[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	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	nsv908080	chr17:34027964-34054044	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9904187	TBC1D29	cis	parietal	SCAN
rs9904187	PEX12	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
3	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
4	chr17:34019000-34044000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:34023200-34043800	Weak transcription	Spleen	Spleen
6	chr17:34023200-34044000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:34023200-34051600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:34023400-34044200	Weak transcription	Brain Germinal Matrix	brain
9	chr17:34024200-34056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:34026600-34050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:34032600-34055800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:34034800-34053400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr17:34034800-34055600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:34035400-34056200	Strong transcription	A549	lung
15	chr17:34035800-34053000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:34036000-34045800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr17:34036000-34047400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr17:34036000-34049000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:34036000-34055600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:34036200-34044000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:34036400-34042600	Weak transcription	Gastric	stomach
22	chr17:34036400-34042600	Weak transcription	Pancreas	Pancrea
23	chr17:34036400-34052200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:34036600-34055800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:34036800-34054800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr17:34037000-34047400	Strong transcription	Primary B cells from cord blood	blood
27	chr17:34037000-34053000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr17:34037200-34042600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:34037200-34044000	Weak transcription	Colon Smooth Muscle	Colon
30	chr17:34037200-34044800	Strong transcription	HMEC	breast
31	chr17:34038000-34044000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:34038600-34043400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr17:34039000-34042600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr17:34039000-34043600	Weak transcription	Brain Angular Gyrus	brain
35	chr17:34039400-34044200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:34039600-34043600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:34039800-34045200	Strong transcription	GM12878-XiMat	blood
38	chr17:34039800-34045800	Genic enhancers	Adipose Nuclei	Adipose
39	chr17:34040000-34043000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:34040000-34043000	Enhancers	Brain Anterior Caudate	brain
41	chr17:34040000-34052800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:34040200-34042800	Genic enhancers	Primary T cells from cord blood	blood
43	chr17:34040200-34055000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:34040400-34043200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:34040400-34043400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:34040400-34043600	Weak transcription	Placenta	Placenta
47	chr17:34040400-34043800	Weak transcription	Right Ventricle	heart
48	chr17:34040400-34044200	Weak transcription	Left Ventricle	heart
49	chr17:34040400-34044600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:34040400-34047200	Weak transcription	Hela-S3	cervix

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