Variant report

Variant	rs3732530
Chromosome Location	chr3:47618953-47618954
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47554458..47556581-chr3:47617891..47619681,2	MCF-7	breast:
2	chr3:47617723..47621182-chr3:47821900..47825077,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1014228	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865948	0.88[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11130138	0.94[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11130139	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11130144	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11130145	0.81[EUR][1000 genomes]
rs11130146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11130148	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs11712152	0.82[EUR][1000 genomes]
rs11712464	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap]
rs11716582	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11929303	0.92[EUR][1000 genomes]
rs12489865	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12492915	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12495204	0.89[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs12498027	0.81[EUR][1000 genomes]
rs12635438	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs12636198	0.96[EUR][1000 genomes]
rs12636863	0.84[EUR][1000 genomes]
rs13061412	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13063042	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs13069142	0.84[EUR][1000 genomes]
rs13081356	0.81[EUR][1000 genomes]
rs13084555	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13085978	0.93[EUR][1000 genomes]
rs13091913	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[TSI][hapmap]
rs13094264	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs1403578	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1403579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1464614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17079785	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2047559	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2049300	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2133601	0.94[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs2140335	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2280567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293226	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2882611	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs34252990	0.86[EUR][1000 genomes]
rs34616865	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35167544	0.90[EUR][1000 genomes]
rs36033865	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3755638	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3772403	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4274776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4858801	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4858835	0.80[EUR][1000 genomes]
rs4858836	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4858842	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4858846	1.00[CEU][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4858851	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs56746603	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs60110914	0.95[EUR][1000 genomes]
rs60322343	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61620099	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61675361	0.93[EUR][1000 genomes]
rs6442070	0.80[EUR][1000 genomes]
rs6442071	0.80[EUR][1000 genomes]
rs6442072	0.87[EUR][1000 genomes]
rs6442082	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs6767896	0.81[EUR][1000 genomes]
rs6768699	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6772301	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs6774170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6777632	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6782707	0.81[EUR][1000 genomes]
rs6784946	0.86[EUR][1000 genomes]
rs6785031	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6785669	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs6786001	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6789835	0.89[EUR][1000 genomes]
rs6792497	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6806860	0.83[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs7429162	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7613934	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7618758	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs7621236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7624474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7631950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7638103	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs7642691	0.89[EUR][1000 genomes]
rs7645846	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs868255	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs869508	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs870622	1.00[CEU][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs883661	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs883662	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs883663	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs9681917	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[TSI][hapmap]
rs9820051	0.80[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	esv3440073	chr3:47618473-47621321	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3732530	MRPS18AP1	cis	lung	GTEx
rs3732530	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs3732530	ZNF589	cis	parietal	SCAN
rs3732530	ATRIP	cis	cerebellum	SCAN
rs3732530	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs3732530	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs3732530	NME6	cis	Esophagus Muscularis	GTEx
rs3732530	SMARCC1	cis	cerebellum	SCAN
rs3732530	HYAL2	cis	cerebellum	SCAN
rs3732530	ZNF589	cis	cerebellum	SCAN
rs3732530	ZNF589	cis	Nerve Tibial	GTEx
rs3732530	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47615800-47619000	Weak transcription	Left Ventricle	heart
2	chr3:47616000-47619000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:47616800-47619000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:47617600-47619200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47617800-47619200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:47618000-47619000	Weak transcription	K562	blood
7	chr3:47618200-47619000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:47618200-47619000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:47618200-47619000	Enhancers	Brain Angular Gyrus	brain
10	chr3:47618200-47619000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:47618200-47619200	Enhancers	Gastric	stomach
12	chr3:47618400-47619000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:47618400-47619000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
14	chr3:47618400-47619000	Bivalent Enhancer	Brain Hippocampus Middle	brain
15	chr3:47618400-47619000	Enhancers	Lung	lung
16	chr3:47618400-47619400	Enhancers	Fetal Brain Male	brain
17	chr3:47618400-47621000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr3:47618600-47619000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr3:47618600-47619000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:47618600-47619000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
21	chr3:47618600-47619200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:47618600-47619200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
23	chr3:47618600-47619200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr3:47618600-47619200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr3:47618600-47619400	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr3:47618600-47619400	Flanking Active TSS	Fetal Brain Female	brain
27	chr3:47618800-47619000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:47618800-47619000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:47618800-47619000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
30	chr3:47618800-47619000	Bivalent Enhancer	Primary B cells from cord blood	blood
31	chr3:47618800-47619000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
32	chr3:47618800-47619000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
33	chr3:47618800-47619000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr3:47618800-47619000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:47618800-47619000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr3:47618800-47619000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
37	chr3:47618800-47619000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:47618800-47619000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:47618800-47619000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:47618800-47619000	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr3:47618800-47619000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:47618800-47619000	Enhancers	Esophagus	oesophagus
43	chr3:47618800-47619000	Bivalent Enhancer	Fetal Intestine Large	intestine
44	chr3:47618800-47619000	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr3:47618800-47619000	Flanking Bivalent TSS/Enh	Placenta	Placenta
46	chr3:47618800-47619000	Bivalent Enhancer	Fetal Stomach	stomach
47	chr3:47618800-47619000	Enhancers	Ovary	ovary
48	chr3:47618800-47619000	Enhancers	Pancreas	Pancrea
49	chr3:47618800-47619000	Enhancers	Spleen	Spleen
50	chr3:47618800-47619000	Bivalent/Poised TSS	HepG2	liver

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