Variant report

Variant	rs13059519
Chromosome Location	chr3:47539969-47539970
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	chr3:47539684-47540157	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:47539572-47540217	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:47539719-47539985	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:47539883-47540051	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:47539772-47539993	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47537303..47543925-chr3:47549598..47557776,11	K562	blood:
2	chr3:47532827..47535628-chr3:47539625..47541232,2	K562	blood:

Variant related genes	Relation type
ENSG00000272110	TF binding region
ENSG00000271161	TF binding region
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1038394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130132	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130133	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11705957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11707895	0.94[EUR][1000 genomes]
rs11710121	0.88[CEU][hapmap]
rs11711265	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11711824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11713413	0.91[EUR][1000 genomes]
rs11716763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719877	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11914795	0.85[EUR][1000 genomes]
rs11914913	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11914932	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11925823	0.81[EUR][1000 genomes]
rs12486969	0.81[EUR][1000 genomes]
rs12489046	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490058	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490383	0.83[JPT][hapmap]
rs12492433	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495169	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12497225	0.82[EUR][1000 genomes]
rs12630641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632132	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064843	0.82[EUR][1000 genomes]
rs13075233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13079098	0.80[EUR][1000 genomes]
rs1531875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1564760	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs17080872	0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs17784882	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs1872164	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2062278	0.82[EUR][1000 genomes]
rs2101247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs295428	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs295433	0.95[YRI][hapmap]
rs295449	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs295458	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs295461	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs34634681	0.94[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816779	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4599332	0.94[EUR][1000 genomes]
rs4858805	0.81[EUR][1000 genomes]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858856	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4858868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56032309	0.82[EUR][1000 genomes]
rs56351005	0.81[EUR][1000 genomes]
rs57346147	0.82[EUR][1000 genomes]
rs59586735	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60369822	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62248599	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62248603	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248605	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260710	0.96[EUR][1000 genomes]
rs62260711	0.96[EUR][1000 genomes]
rs62260741	0.91[EUR][1000 genomes]
rs6765990	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780013	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs6787422	0.82[EUR][1000 genomes]
rs6790763	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6792461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792488	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73081205	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7628631	0.99[EUR][1000 genomes]
rs7649234	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651194	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs807932	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs878659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs922957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs9683033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9683177	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs13059519	C3orf75	cis	cerebellum	SCAN
rs13059519	AMIGO3	cis	cerebellum	SCAN
rs13059519	CCDC12	cis	cerebellum	SCAN
rs13059519	SCAP	cis	parietal	SCAN
rs13059519	HYAL2	cis	cerebellum	SCAN
rs13059519	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs13059519	PRKAR2A	cis	cerebellum	SCAN
rs13059519	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs13059519	NCKIPSD	cis	cerebellum	SCAN
rs13059519	RTP3	cis	lesional skin	skin_eQTL
rs13059519	IFRD2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47517800-47544400	Weak transcription	Small Intestine	intestine
2	chr3:47518200-47541600	Weak transcription	Fetal Kidney	kidney
3	chr3:47532000-47546400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47532600-47542200	Weak transcription	Fetal Brain Male	brain
5	chr3:47533600-47542200	Weak transcription	HUVEC	blood vessel
6	chr3:47534200-47547000	Strong transcription	Dnd41	blood
7	chr3:47534400-47543000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47534400-47546000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:47534400-47546200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:47534600-47546000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:47534600-47553000	Strong transcription	Fetal Thymus	thymus
12	chr3:47534800-47549400	Weak transcription	Fetal Heart	heart
13	chr3:47534800-47552400	Strong transcription	Fetal Intestine Small	intestine
14	chr3:47534800-47553200	Strong transcription	Fetal Stomach	stomach
15	chr3:47535200-47543000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:47535200-47546200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:47535200-47546200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:47535200-47546200	Strong transcription	Thymus	Thymus
19	chr3:47535200-47547000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:47535200-47553000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:47535400-47546400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:47535400-47546400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:47535400-47546400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:47535600-47546600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:47535600-47547000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:47535600-47552800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:47535800-47546600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:47536000-47541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:47536200-47544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:47536200-47546400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:47536200-47553200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:47536400-47546000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:47536400-47546000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:47536400-47546200	Strong transcription	Liver	Liver
35	chr3:47536400-47546400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:47536400-47546400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:47536400-47546800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:47536400-47547000	Strong transcription	HepG2	liver
39	chr3:47536600-47540400	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr3:47536600-47543200	Strong transcription	HSMMtube	muscle
41	chr3:47536600-47543400	Strong transcription	Ovary	ovary
42	chr3:47536600-47544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:47536600-47544400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:47536600-47546000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:47536600-47546000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:47536600-47546000	Strong transcription	Colonic Mucosa	Colon
47	chr3:47536600-47546000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:47536600-47546000	Strong transcription	Left Ventricle	heart
49	chr3:47536600-47546000	Strong transcription	Pancreas	Pancrea
50	chr3:47536600-47546000	Strong transcription	GM12878-XiMat	blood

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