Variant report

Variant	rs12608517
Chromosome Location	chr19:36558113-36558114
allele	C/T
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	POLR2A	chr19:36557707-36558211	K562	blood:	n/a	n/a
2	POLR2A	chr19:36557952-36558265	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36544205..36547334-chr19:36557272..36560245,4	K562	blood:

Variant related genes	Relation type
WDR62	TF binding region
ENSG00000075702	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009381	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs10406862	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10418079	0.85[YRI][hapmap]
rs10419924	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10420345	0.89[ASN][1000 genomes]
rs10421377	0.83[ASN][1000 genomes]
rs10422055	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs10425700	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10427033	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11538454	1.00[ASN][1000 genomes]
rs11666192	0.93[ASN][1000 genomes]
rs11669890	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12462159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12981698	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs2023866	0.88[ASN][1000 genomes]
rs2074435	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2141959	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2227260	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2231568	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2285745	0.81[TSI][hapmap]
rs2301734	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2301737	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2871649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4555271	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806249	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4806262	0.89[ASN][1000 genomes]
rs4806271	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4806273	0.85[ASN][1000 genomes]
rs4806276	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55849299	0.98[ASN][1000 genomes]
rs6510516	0.94[YRI][hapmap]
rs7250364	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257026	0.81[ASN][1000 genomes]
rs7258807	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];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73036134	0.92[ASN][1000 genomes]
rs8112640	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12608517	ZFP36	cis	parietal	SCAN
rs12608517	PHLDB3	cis	cerebellum	SCAN
rs12608517	ZNF527	cis	cerebellum	SCAN
rs12608517	ZNF420	cis	cerebellum	SCAN
rs12608517	CYP2A7	cis	parietal	SCAN
rs12608517	PHLDB3	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36572400	Weak transcription	Lung	lung
4	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
5	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
10	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:36547000-36561200	Weak transcription	NH-A	brain
14	chr19:36547400-36561200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:36547400-36562000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:36547600-36559200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36547600-36559200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
19	chr19:36548000-36559200	Strong transcription	Fetal Thymus	thymus
20	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr19:36548400-36559200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:36548400-36559200	Strong transcription	A549	lung
23	chr19:36548400-36571000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:36548600-36559400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:36548600-36560800	Weak transcription	HUVEC	blood vessel
26	chr19:36548800-36559200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:36548800-36560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:36548800-36567800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:36549200-36559400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:36549200-36559400	Strong transcription	Fetal Stomach	stomach
31	chr19:36549400-36558800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:36549400-36558800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr19:36549400-36559200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:36549400-36559200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:36549400-36559200	Strong transcription	Thymus	Thymus
36	chr19:36549400-36559400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:36549400-36560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:36549600-36559200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:36549600-36559400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:36549600-36566600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:36549600-36567200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:36549800-36558600	Weak transcription	Gastric	stomach
43	chr19:36550200-36559800	Strong transcription	Dnd41	blood
44	chr19:36551600-36558400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:36551800-36559200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:36552000-36561600	Weak transcription	Brain Angular Gyrus	brain
47	chr19:36552000-36572400	Weak transcription	Liver	Liver
48	chr19:36554200-36558800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:36554200-36559200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:36554200-36559200	Strong transcription	Fetal Muscle Trunk	muscle

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