Variant report

Variant	rs226434
Chromosome Location	chr17:34043021-34043022
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	chr17:34037578..34041296-chr17:34042610..34046006,5	K562	blood:

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

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

rs_ID	r²[population]
rs12150359	0.84[ASN][1000 genomes]
rs12949341	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1634684	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs170483	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225255	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs225284	0.82[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs225290	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs225297	0.82[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs226085	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs226086	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226091	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs226426	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226428	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226429	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226432	0.84[ASN][1000 genomes]
rs226439	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];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226441	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2285742	0.84[ASN][1000 genomes]
rs321596	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs321599	0.81[ASW][hapmap];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	0.82[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3890901	0.84[ASN][1000 genomes]
rs4796103	0.84[ASN][1000 genomes]
rs6505489	0.84[ASN][1000 genomes]
rs6505490	0.83[ASN][1000 genomes]
rs6505491	0.84[ASN][1000 genomes]
rs6505492	0.84[ASN][1000 genomes]
rs6505493	0.84[ASN][1000 genomes]
rs67296463	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71366475	0.83[ASN][1000 genomes]
rs720774	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7217565	0.84[ASN][1000 genomes]
rs7221081	0.84[ASN][1000 genomes]
rs7221096	0.84[ASN][1000 genomes]
rs7406966	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs8064556	0.84[ASN][1000 genomes]
rs8067294	0.84[ASN][1000 genomes]
rs8073375	0.84[ASN][1000 genomes]
rs8078905	0.82[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	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
rs226434	PEX12	cis	cerebellum	SCAN
rs226434	TBC1D29	cis	parietal	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	chr17:34036400-34052200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:34036600-34055800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:34036800-34054800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:34037000-34047400	Strong transcription	Primary B cells from cord blood	blood
25	chr17:34037000-34053000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr17:34037200-34044000	Weak transcription	Colon Smooth Muscle	Colon
27	chr17:34037200-34044800	Strong transcription	HMEC	breast
28	chr17:34038000-34044000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:34038600-34043400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:34039000-34043600	Weak transcription	Brain Angular Gyrus	brain
31	chr17:34039400-34044200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:34039600-34043600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:34039800-34045200	Strong transcription	GM12878-XiMat	blood
34	chr17:34039800-34045800	Genic enhancers	Adipose Nuclei	Adipose
35	chr17:34040000-34052800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:34040200-34055000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr17:34040400-34043200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:34040400-34043400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:34040400-34043600	Weak transcription	Placenta	Placenta
40	chr17:34040400-34043800	Weak transcription	Right Ventricle	heart
41	chr17:34040400-34044200	Weak transcription	Left Ventricle	heart
42	chr17:34040400-34044600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:34040400-34047200	Weak transcription	Hela-S3	cervix
44	chr17:34040400-34049200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:34040400-34054400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:34040600-34043600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:34040600-34043600	Weak transcription	Small Intestine	intestine
48	chr17:34040600-34043600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr17:34040600-34043600	Weak transcription	Thymus	Thymus
50	chr17:34040600-34043800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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