Variant report

Variant	rs12500426
Chromosome Location	chr4:95514609-95514610
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95508126..95511590-chr4:95512972..95515288,3	K562	blood:
2	chr4:95508126..95510888-chr4:95512972..95515677,3	K562	blood:
3	chr4:95373466..95376554-chr4:95514492..95517444,3	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10019142	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10019505	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033326	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10034824	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724023	0.85[CEU][hapmap]
rs11732687	0.85[CEU][hapmap]
rs12639623	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639887	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12642449	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12645971	0.81[CHB][hapmap]
rs12648941	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649976	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs13110115	0.82[CHB][hapmap]
rs13122786	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs13135257	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs13143502	0.84[CHB][hapmap]
rs2047025	0.85[CEU][hapmap]
rs2172448	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452010	0.82[CHB][hapmap]
rs2452571	0.86[CHB][hapmap]
rs2452574	0.82[CHB][hapmap]
rs2452575	0.81[CHB][hapmap]
rs2452578	0.86[CHB][hapmap]
rs2452580	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2452589	0.86[ASN][1000 genomes]
rs2452601	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2510769	0.95[CHB][hapmap]
rs2510772	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2510777	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2510781	0.82[CHB][hapmap]
rs28740868	0.90[ASN][1000 genomes]
rs3805263	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs3805264	0.81[ASN][1000 genomes]
rs3805266	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3843444	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4634230	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699505	0.81[CHB][hapmap]
rs5013417	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs60063444	0.83[ASN][1000 genomes]
rs6532491	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854173	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7662466	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs902981	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs973995	0.81[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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	19767753	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12500426	PDLIM5	cis	parietal	SCAN
rs12500426	ATOH1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
5	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
6	chr4:95497200-95516200	Weak transcription	Right Atrium	heart
7	chr4:95497200-95520000	Weak transcription	Spleen	Spleen
8	chr4:95497200-95524600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:95497200-95524600	Weak transcription	Gastric	stomach
10	chr4:95497200-95524600	Weak transcription	Lung	lung
11	chr4:95497200-95526000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
14	chr4:95497400-95515000	Weak transcription	Colonic Mucosa	Colon
15	chr4:95497400-95524200	Weak transcription	NHLF	lung
16	chr4:95497400-95526200	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:95497400-95542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:95497600-95539200	Weak transcription	HepG2	liver
19	chr4:95498400-95526200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:95499000-95516400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:95499800-95515400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:95503200-95516000	Weak transcription	Stomach Mucosa	stomach
23	chr4:95504600-95517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:95505000-95515000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:95505200-95516800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:95505400-95515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:95505600-95517000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:95505800-95516000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:95506600-95514800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:95507200-95548200	Weak transcription	Psoas Muscle	Psoas
31	chr4:95507200-95548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:95507400-95515400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:95507400-95515800	Weak transcription	Fetal Stomach	stomach
34	chr4:95507400-95516000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:95507600-95516000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:95507800-95516000	Weak transcription	K562	blood
37	chr4:95507800-95521000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:95507800-95539200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:95508000-95515800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:95508200-95526000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:95508400-95516000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:95509400-95515800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:95510600-95524800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:95511000-95515000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:95511000-95515000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr4:95511200-95554800	Weak transcription	NHDF-Ad	bronchial
47	chr4:95511800-95514800	Genic enhancers	Left Ventricle	heart
48	chr4:95511800-95515200	Strong transcription	HUVEC	blood vessel
49	chr4:95511800-95515600	Strong transcription	Osteobl	bone
50	chr4:95512000-95515000	Strong transcription	Liver	Liver

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