Variant report

Variant	rs13094438
Chromosome Location	chr3:47277885-47277886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47276902..47279384-chr3:47323090..47325567,2	K562	blood:
2	chr3:47276373..47278773-chr3:47281395..47283848,2	K562	blood:
3	chr3:47261367..47263490-chr3:47277485..47279613,2	K562	blood:
4	chr3:47276538..47278116-chr3:47285524..47288270,2	K562	blood:

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap]
rs1076394	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap]
rs11130114	0.84[ASN][1000 genomes]
rs11130115	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs11130123	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11705957	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11708451	0.86[ASN][1000 genomes]
rs11710013	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11711824	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap]
rs11712445	0.95[CEU][hapmap]
rs11712716	0.85[ASN][1000 genomes]
rs11714294	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11716539	0.85[ASN][1000 genomes]
rs11718795	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719306	0.82[ASN][1000 genomes]
rs11719877	0.96[CEU][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs11915074	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11920354	0.87[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11921117	0.81[EUR][1000 genomes]
rs11925560	0.86[EUR][1000 genomes]
rs12488225	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489211	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12629262	0.83[ASN][1000 genomes]
rs12635619	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs13061071	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs13062022	0.85[ASN][1000 genomes]
rs13063250	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap]
rs13078131	0.81[ASN][1000 genomes]
rs13084117	0.85[ASN][1000 genomes]
rs13094672	0.84[ASN][1000 genomes]
rs13098228	0.83[ASN][1000 genomes]
rs1531875	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs1638676	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17410853	0.85[CEU][hapmap]
rs17411375	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs17476234	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2088135	0.90[EUR][1000 genomes]
rs2132173	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159400	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295428	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs295441	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295449	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs295458	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs295461	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs3736177	0.95[CEU][hapmap]
rs4078466	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4082155	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs4682852	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4683320	0.84[ASN][1000 genomes]
rs4683322	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs4683324	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683326	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs56250009	0.90[EUR][1000 genomes]
rs62248905	0.89[EUR][1000 genomes]
rs6767907	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs6768221	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6780013	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs6785790	0.84[ASN][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs73069104	0.81[EUR][1000 genomes]
rs7615323	0.85[ASN][1000 genomes]
rs7621911	0.80[ASN][1000 genomes]
rs7632501	0.88[EUR][1000 genomes]
rs7636423	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs807935	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs807936	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs807937	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9837343	0.81[CEU][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1799921	chr3:47259253-47283105	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13094438	PRKAR2A	cis	cerebellum	SCAN
rs13094438	SCAP	cis	parietal	SCAN
rs13094438	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs13094438	HYAL2	cis	cerebellum	SCAN
rs13094438	NCKIPSD	cis	cerebellum	SCAN
rs13094438	RTP3	cis	lesional skin	skin_eQTL
rs13094438	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs13094438	AMIGO3	cis	cerebellum	SCAN
rs13094438	CCDC12	cis	cerebellum	SCAN
rs13094438	C3orf75	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:47264200-47322200	Weak transcription	Gastric	stomach
3	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:47267400-47281400	Weak transcription	Fetal Stomach	stomach
7	chr3:47267400-47284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:47269800-47281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:47269800-47281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:47270000-47284600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:47270600-47286800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:47271200-47281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:47276200-47283000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:47276600-47283800	Weak transcription	Right Ventricle	heart
22	chr3:47276800-47281400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:47276800-47284000	Weak transcription	HSMMtube	muscle
24	chr3:47276800-47284600	Weak transcription	Pancreas	Pancrea
25	chr3:47276800-47285200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:47276800-47285200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:47277000-47281400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:47277000-47288200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:47277000-47292000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:47277200-47281800	Weak transcription	HepG2	liver
31	chr3:47277400-47284600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:47277400-47285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:47277600-47281600	Weak transcription	Lung	lung
34	chr3:47277600-47300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:47277800-47278400	Strong transcription	Fetal Muscle Trunk	muscle

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