Variant report

Variant	rs226439
Chromosome Location	chr17:34036690-34036691
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	chr17:33414339..33416921-chr17:34036164..34038163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092871	Chromatin interaction

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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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]
rs226085	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs226086	0.97[AFR][1000 genomes];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[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs226091	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226428	0.83[ASW][hapmap];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]
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];0.82[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];1.00[YRI][hapmap];0.90[AFR][1000 genomes];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	0.86[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	0.84[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	0.94[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];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
rs226439	TBC1D29	cis	parietal	SCAN
rs226439	PEX12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
4	chr17:34002000-34036800	Weak transcription	Colonic Mucosa	Colon
5	chr17:34006600-34039800	Weak transcription	Small Intestine	intestine
6	chr17:34017800-34040400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
8	chr17:34019000-34044000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:34021000-34036800	Weak transcription	NHEK	skin
10	chr17:34021200-34037000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:34022200-34042400	Weak transcription	Aorta	Aorta
12	chr17:34023000-34036800	Weak transcription	NHDF-Ad	bronchial
13	chr17:34023200-34036800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr17:34023200-34037000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:34023200-34037400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:34023200-34043800	Weak transcription	Spleen	Spleen
17	chr17:34023200-34044000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:34023200-34051600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr17:34023400-34036800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:34023400-34044200	Weak transcription	Brain Germinal Matrix	brain
21	chr17:34023600-34036800	Weak transcription	Brain Substantia Nigra	brain
22	chr17:34023600-34037000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:34023600-34037000	Weak transcription	Fetal Brain Female	brain
24	chr17:34023800-34039000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:34024200-34056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr17:34024400-34036800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:34024600-34037200	Weak transcription	Brain Hippocampus Middle	brain
28	chr17:34026600-34039600	Weak transcription	HSMMtube	muscle
29	chr17:34026600-34050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:34028200-34037200	Weak transcription	HMEC	breast
31	chr17:34028600-34036800	Weak transcription	NH-A	brain
32	chr17:34031200-34037000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr17:34032600-34055800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr17:34033600-34037000	Weak transcription	HepG2	liver
35	chr17:34034600-34037200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr17:34034600-34041000	Strong transcription	Dnd41	blood
37	chr17:34034800-34037800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr17:34034800-34053400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:34034800-34055600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr17:34035000-34037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:34035000-34037000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr17:34035000-34037400	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr17:34035000-34039600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:34035200-34037000	Weak transcription	Brain Angular Gyrus	brain
45	chr17:34035200-34037200	Enhancers	Fetal Heart	heart
46	chr17:34035400-34037400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:34035400-34037400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:34035400-34039200	Strong transcription	HSMM	muscle
49	chr17:34035400-34056200	Strong transcription	A549	lung
50	chr17:34035600-34036800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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