Variant report

Variant	rs12150359
Chromosome Location	chr17:34024584-34024585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34024050..34027708-chr17:34038047..34041626,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1049379	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12949341	0.85[ASN][1000 genomes]
rs1476553	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161182	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161183	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161184	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1634684	0.82[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];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs170483	0.84[ASN][1000 genomes]
rs178649	0.85[EUR][1000 genomes]
rs225245	0.89[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs225255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs225269	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225272	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225273	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225281	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225282	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs225284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225293	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225299	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225302	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226085	0.83[ASN][1000 genomes]
rs226086	0.85[ASN][1000 genomes]
rs226088	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs226426	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226428	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226432	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs226434	0.82[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs226439	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs226441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301730	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs321596	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs321599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs321601	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs321607	0.81[CEU][hapmap]
rs321616	0.85[CEU][hapmap]
rs321617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs321618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3890901	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795085	0.86[EUR][1000 genomes]
rs4796103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505490	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505491	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505492	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505493	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67296463	0.83[ASN][1000 genomes]
rs71366475	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7217565	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221081	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221096	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7406966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8064556	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067294	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073375	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8078905	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9635770	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12150359	AP2B1	cis	Muscle Skeletal	GTEx
rs12150359	TBC1D29	cis	parietal	SCAN
rs12150359	TBC1D29	cis	cerebellum	SCAN
rs12150359	SLFN5	cis	parietal	SCAN
rs12150359	PEX12	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr17:33992800-34028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:33995800-34024600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:33997600-34024600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
9	chr17:34002000-34032200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:34002000-34036800	Weak transcription	Colonic Mucosa	Colon
11	chr17:34005400-34028400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:34005800-34026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:34006600-34032800	Weak transcription	Stomach Mucosa	stomach
14	chr17:34006600-34039800	Weak transcription	Small Intestine	intestine
15	chr17:34011000-34026600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:34011800-34036200	Weak transcription	Hela-S3	cervix
17	chr17:34013600-34036000	Weak transcription	NHLF	lung
18	chr17:34014600-34024800	Strong transcription	Primary B cells from cord blood	blood
19	chr17:34014800-34024600	Strong transcription	K562	blood
20	chr17:34016000-34036600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:34017200-34034600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:34017600-34024600	Strong transcription	HMEC	breast
23	chr17:34017800-34040400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:34018800-34034600	Weak transcription	Pancreas	Pancrea
25	chr17:34018800-34036000	Weak transcription	Gastric	stomach
26	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
27	chr17:34019000-34044000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:34020000-34024600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:34020800-34024800	Strong transcription	Lung	lung
30	chr17:34021000-34036800	Weak transcription	NHEK	skin
31	chr17:34021200-34025800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr17:34021200-34037000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr17:34021800-34024600	Strong transcription	HSMMtube	muscle
34	chr17:34022000-34036000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:34022000-34036200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:34022200-34036000	Weak transcription	Ovary	ovary
37	chr17:34022200-34042400	Weak transcription	Aorta	Aorta
38	chr17:34022400-34036000	Weak transcription	Left Ventricle	heart
39	chr17:34022600-34035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr17:34022600-34036000	Weak transcription	Psoas Muscle	Psoas
41	chr17:34022800-34036000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:34022800-34036200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:34022800-34036400	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:34023000-34034800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr17:34023000-34034800	Weak transcription	Brain Angular Gyrus	brain
46	chr17:34023000-34035200	Weak transcription	GM12878-XiMat	blood
47	chr17:34023000-34036800	Weak transcription	NHDF-Ad	bronchial
48	chr17:34023200-34026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr17:34023200-34028600	Weak transcription	Right Atrium	heart
50	chr17:34023200-34031200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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