Variant report

Variant	rs226085
Chromosome Location	chr17:34019488-34019489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12150359	0.83[ASN][1000 genomes]
rs12949341	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1634684	0.83[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs170483	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225255	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs225284	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs225290	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs225297	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs226086	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226091	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226428	0.83[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226429	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs226432	0.83[ASN][1000 genomes]
rs226434	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs226439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs226441	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2285742	0.84[ASN][1000 genomes]
rs321596	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs321599	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs321601	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs321617	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs321618	0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3890901	0.84[ASN][1000 genomes]
rs4796103	0.83[ASN][1000 genomes]
rs6505489	0.83[ASN][1000 genomes]
rs6505490	0.82[ASN][1000 genomes]
rs6505491	0.83[ASN][1000 genomes]
rs6505492	0.83[ASN][1000 genomes]
rs6505493	0.83[ASN][1000 genomes]
rs67296463	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71366475	0.82[ASN][1000 genomes]
rs720774	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7217565	0.83[ASN][1000 genomes]
rs7221081	0.83[ASN][1000 genomes]
rs7221096	0.83[ASN][1000 genomes]
rs7406966	0.94[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8064556	0.84[ASN][1000 genomes]
rs8067294	0.83[ASN][1000 genomes]
rs8073375	0.84[ASN][1000 genomes]
rs8078905	0.83[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs226085	PEX12	cis	cerebellum	SCAN
rs226085	TBC1D29	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr17:33992800-34028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:33995800-34024600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:33997400-34023200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:33997600-34024600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
11	chr17:34002000-34032200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:34002000-34036800	Weak transcription	Colonic Mucosa	Colon
13	chr17:34005400-34024400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:34005400-34028400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:34005600-34024400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:34005800-34026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:34006000-34024400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:34006400-34024200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:34006600-34032800	Weak transcription	Stomach Mucosa	stomach
20	chr17:34006600-34039800	Weak transcription	Small Intestine	intestine
21	chr17:34011000-34021800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:34011000-34022400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr17:34011000-34026600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr17:34011200-34024400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr17:34011600-34021000	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:34011800-34022400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:34011800-34036200	Weak transcription	Hela-S3	cervix
28	chr17:34012000-34020800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:34012000-34021800	Weak transcription	HSMMtube	muscle
30	chr17:34012000-34022400	Weak transcription	Psoas Muscle	Psoas
31	chr17:34012000-34024400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:34012200-34024400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:34012200-34024400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:34012400-34019600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:34012400-34022200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:34012400-34022600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr17:34012800-34020400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:34013600-34036000	Weak transcription	NHLF	lung
39	chr17:34014000-34023200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:34014600-34021800	Weak transcription	Right Ventricle	heart
41	chr17:34014600-34024800	Strong transcription	Primary B cells from cord blood	blood
42	chr17:34014800-34020200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:34014800-34024600	Strong transcription	K562	blood
44	chr17:34015000-34020200	Strong transcription	NHEK	skin
45	chr17:34015400-34022000	Weak transcription	Brain Substantia Nigra	brain
46	chr17:34015400-34022000	Weak transcription	Fetal Brain Female	brain
47	chr17:34015400-34022400	Strong transcription	Left Ventricle	heart
48	chr17:34015800-34020800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr17:34015800-34022600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr17:34016000-34036600	Weak transcription	Brain Cingulate Gyrus	brain

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