Variant report

Variant	rs524986
Chromosome Location	chr3:52228496-52228497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52209128..52211243-chr3:52227235..52228874,2	MCF-7	breast:
2	chr3:52087390..52089445-chr3:52228138..52231082,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs104903	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap]
rs11712164	0.86[CHB][hapmap]
rs11717383	0.80[CHB][hapmap]
rs164640	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs181274	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187084	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs352139	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs352140	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs352158	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352161	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352162	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352163	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352165	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352167	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352168	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352169	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352170	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352171	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs411457	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap]
rs614288	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap]
rs7614727	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs524986	NEK4	cis	cerebellum	SCAN
rs524986	SEMA3G	cis	cerebellum	SCAN
rs524986	NT5DC2	cis	lymphoblastoid	seeQTL
rs524986	NEK4	cis	parietal	SCAN
rs524986	GNL3	cis	cerebellum	SCAN
rs524986	DNAH1	cis	cerebellum	SCAN
rs524986	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs524986	NT5DC2	cis	cerebellum	SCAN
rs524986	GNL3	cis	parietal	SCAN
rs524986	SPCS1	cis	parietal	SCAN
rs524986	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs524986	ITIH4	cis	parietal	SCAN
rs524986	GLYCTK	cis	parietal	SCAN
rs524986	RBM6	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52218800-52229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:52220200-52230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52222200-52231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:52224000-52230000	Enhancers	Ovary	ovary
6	chr3:52224600-52230800	Weak transcription	Psoas Muscle	Psoas
7	chr3:52224800-52229400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:52224800-52229400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52224800-52229800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:52224800-52231400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52225000-52229400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52225000-52229800	Weak transcription	Left Ventricle	heart
13	chr3:52225000-52231400	Weak transcription	NH-A	brain
14	chr3:52225200-52229000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:52225400-52229200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:52225400-52229400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:52225400-52231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:52225400-52231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:52225400-52231200	Weak transcription	Pancreas	Pancrea
20	chr3:52225400-52231200	Weak transcription	Right Atrium	heart
21	chr3:52225800-52231200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:52226000-52229200	Weak transcription	K562	blood
23	chr3:52226600-52231600	Enhancers	Placenta	Placenta
24	chr3:52226800-52231600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:52226800-52232000	Enhancers	Spleen	Spleen
26	chr3:52227000-52230000	Enhancers	Lung	lung
27	chr3:52227400-52229400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:52227400-52229400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:52227400-52229600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:52227400-52229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:52227400-52230800	Weak transcription	Gastric	stomach
32	chr3:52227400-52231400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:52227400-52231600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:52227400-52231600	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:52227600-52229200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:52227600-52229200	Weak transcription	Right Ventricle	heart
37	chr3:52227600-52229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:52227600-52229400	Weak transcription	NHDF-Ad	bronchial
39	chr3:52227600-52229400	Weak transcription	NHLF	lung
40	chr3:52227600-52229600	Weak transcription	Hela-S3	cervix
41	chr3:52227600-52229600	Weak transcription	Osteobl	bone
42	chr3:52227600-52229800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:52227600-52229800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:52227600-52229800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:52227600-52229800	Weak transcription	Adipose Nuclei	Adipose
46	chr3:52227600-52229800	Weak transcription	Liver	Liver
47	chr3:52227600-52229800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:52227600-52230000	Weak transcription	HMEC	breast
49	chr3:52227600-52230800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:52227600-52230800	Weak transcription	Brain Cingulate Gyrus	brain

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