Variant report

Variant	rs17784882
Chromosome Location	chr3:47544003-47544004
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47446673..47448536-chr3:47543472..47546163,2	K562	blood:
2	chr3:47517236..47519106-chr3:47543060..47545522,2	K562	blood:
3	chr3:47543403..47546358-chr3:47552663..47555056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000114650	Chromatin interaction
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[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10865946	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs11130132	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130133	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11705957	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs11707895	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11710121	0.88[CEU][hapmap]
rs11711265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711824	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs11712445	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11713413	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716763	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes]
rs11719877	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11914795	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11914913	0.96[EUR][1000 genomes]
rs11914932	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11925823	0.82[EUR][1000 genomes]
rs12486969	0.82[EUR][1000 genomes]
rs12489046	0.92[EUR][1000 genomes]
rs12490058	0.98[EUR][1000 genomes]
rs12492433	0.92[EUR][1000 genomes]
rs12497225	0.83[EUR][1000 genomes]
rs12630641	0.98[EUR][1000 genomes]
rs12632132	0.83[EUR][1000 genomes]
rs12636851	0.80[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs13059519	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs13064843	0.82[EUR][1000 genomes]
rs13075233	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs13079098	0.81[EUR][1000 genomes]
rs1531875	1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1564760	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1564761	0.88[ASN][1000 genomes]
rs17410853	0.85[ASW][hapmap];0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap]
rs1872164	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs1872166	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2062278	0.83[EUR][1000 genomes]
rs2101247	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295428	0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap]
rs295449	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs295458	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs295461	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs34634681	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3816779	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4599332	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858805	0.81[EUR][1000 genomes]
rs4858811	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.80[EUR][1000 genomes]
rs4858856	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858868	1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap]
rs4858894	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs56032309	0.83[EUR][1000 genomes]
rs56351005	0.81[EUR][1000 genomes]
rs57346147	0.83[EUR][1000 genomes]
rs59586735	0.93[EUR][1000 genomes]
rs60369822	0.88[EUR][1000 genomes]
rs62248599	0.91[EUR][1000 genomes]
rs62248603	0.87[EUR][1000 genomes]
rs62248605	0.94[EUR][1000 genomes]
rs62260710	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260711	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260741	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6765990	0.99[EUR][1000 genomes]
rs6768879	0.83[ASN][1000 genomes]
rs6780013	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap]
rs6787422	0.82[EUR][1000 genomes]
rs6790763	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792461	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs6792488	0.89[EUR][1000 genomes]
rs6800271	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs73081205	0.91[EUR][1000 genomes]
rs7628631	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649234	0.90[EUR][1000 genomes]
rs7651194	0.99[EUR][1000 genomes]
rs7651762	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs807932	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs878659	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs922957	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs9683033	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs9683177	0.90[EUR][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

Variant related diseases (count:1)

Disease	PMID	Source
QT interval	24952745	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17784882	AMIGO3	cis	cerebellum	SCAN
rs17784882	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs17784882	CCDC12	cis	cerebellum	SCAN
rs17784882	NCKIPSD	cis	cerebellum	SCAN
rs17784882	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs17784882	IFRD2	cis	parietal	SCAN
rs17784882	SCAP	cis	parietal	SCAN
rs17784882	C3orf75	cis	cerebellum	SCAN
rs17784882	HYAL2	cis	cerebellum	SCAN
rs17784882	PRKAR2A	cis	cerebellum	SCAN

Chromatin state (count:127 , 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	chr3:47532000-47546400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:47534200-47547000	Strong transcription	Dnd41	blood
4	chr3:47534400-47546000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47534400-47546200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:47534600-47546000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:47534600-47553000	Strong transcription	Fetal Thymus	thymus
8	chr3:47534800-47549400	Weak transcription	Fetal Heart	heart
9	chr3:47534800-47552400	Strong transcription	Fetal Intestine Small	intestine
10	chr3:47534800-47553200	Strong transcription	Fetal Stomach	stomach
11	chr3:47535200-47546200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:47535200-47546200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47535200-47546200	Strong transcription	Thymus	Thymus
14	chr3:47535200-47547000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:47535200-47553000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:47535400-47546400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr3:47535400-47546400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:47535400-47546400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:47535600-47546600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:47535600-47547000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:47535600-47552800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:47535800-47546600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:47536200-47546400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:47536200-47553200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:47536400-47546000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:47536400-47546000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:47536400-47546200	Strong transcription	Liver	Liver
28	chr3:47536400-47546400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:47536400-47546400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:47536400-47546800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:47536400-47547000	Strong transcription	HepG2	liver
32	chr3:47536600-47544400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:47536600-47546000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:47536600-47546000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:47536600-47546000	Strong transcription	Colonic Mucosa	Colon
36	chr3:47536600-47546000	Strong transcription	Fetal Intestine Large	intestine
37	chr3:47536600-47546000	Strong transcription	Left Ventricle	heart
38	chr3:47536600-47546000	Strong transcription	Pancreas	Pancrea
39	chr3:47536600-47546000	Strong transcription	GM12878-XiMat	blood
40	chr3:47536600-47546000	Strong transcription	NHLF	lung
41	chr3:47536600-47546000	Strong transcription	Osteobl	bone
42	chr3:47536600-47546200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:47536600-47546200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:47536600-47546200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:47536600-47546200	Strong transcription	Adipose Nuclei	Adipose
46	chr3:47536600-47546200	Strong transcription	Aorta	Aorta
47	chr3:47536600-47546200	Strong transcription	Brain Anterior Caudate	brain
48	chr3:47536600-47546200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:47536600-47546200	Strong transcription	Placenta	Placenta
50	chr3:47536600-47546200	Strong transcription	Gastric	stomach

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