Variant report

Variant	rs13524
Chromosome Location	chr1:114228200-114228201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114225725..114228259-chr1:114231817..114234548,2	MCF-7	breast:
2	chr1:114228136..114230531-chr1:114234621..114236141,2	K562	blood:
3	chr1:114221190..114223803-chr1:114226200..114229279,3	MCF-7	breast:
4	chr1:114226647..114228206-chr11:59448085..59449746,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10776773	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10858006	0.86[ASN][1000 genomes]
rs10858015	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11102667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102671	0.88[AFR][1000 genomes]
rs11102678	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1146183	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1146184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146185	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026423	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12138638	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12144309	0.81[GIH][hapmap]
rs1217194	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1217202	0.86[ASN][1000 genomes]
rs1217212	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1217224	0.88[ASN][1000 genomes]
rs1217225	0.87[ASW][hapmap];0.95[YRI][hapmap]
rs1217229	0.86[ASN][1000 genomes]
rs1217231	0.95[YRI][hapmap]
rs1217238	0.81[ASN][1000 genomes]
rs1217375	0.93[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs1217379	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs1217403	0.85[CHB][hapmap]
rs1217406	0.82[YRI][hapmap]
rs1217408	0.85[CHB][hapmap];0.83[YRI][hapmap]
rs1217414	1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs1217419	0.83[YRI][hapmap]
rs1230673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1230675	0.83[ASN][1000 genomes]
rs1230681	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1230684	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1235000	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs1237290	0.86[ASN][1000 genomes]
rs12757859	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343630	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs1624335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1743594	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1743595	0.88[ASN][1000 genomes]
rs1777239	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1935836	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1970559	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs2040041	1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap]
rs2185827	0.82[CHB][hapmap]
rs2476599	0.93[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs2476600	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs2476602	0.93[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap]
rs2636003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2797416	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs2798137	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789597	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7522138	0.80[ASW][hapmap]
rs7543121	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555634	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs9429525	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13524	MAGI3	cis	cerebellum	SCAN
rs13524	AP4B1	cis	cerebellum	SCAN
rs13524	RAP1A	cis	parietal	SCAN
rs13524	PHTF1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
2	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
4	chr1:114183000-114235800	Weak transcription	Dnd41	blood
5	chr1:114202000-114241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:114203000-114232000	Weak transcription	Fetal Brain Female	brain
7	chr1:114203000-114237800	Weak transcription	NH-A	brain
8	chr1:114203200-114232200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:114203200-114237600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
11	chr1:114203400-114237800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:114206600-114229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:114207400-114230600	Weak transcription	NHEK	skin
14	chr1:114209600-114229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:114209800-114232400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:114211200-114231400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:114211600-114234600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:114213600-114232000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:114213600-114241600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:114214800-114232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:114215400-114235800	Weak transcription	Esophagus	oesophagus
22	chr1:114215400-114235800	Weak transcription	Lung	lung
23	chr1:114216000-114247000	Weak transcription	HMEC	breast
24	chr1:114216200-114241600	Weak transcription	Pancreas	Pancrea
25	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:114216400-114232000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:114216400-114250400	Weak transcription	Placenta	Placenta
28	chr1:114218000-114235800	Weak transcription	Psoas Muscle	Psoas
29	chr1:114218200-114240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:114220200-114229600	Weak transcription	Osteobl	bone
31	chr1:114220200-114232200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:114220400-114263800	Weak transcription	Fetal Kidney	kidney
33	chr1:114220600-114234400	Weak transcription	HSMMtube	muscle
34	chr1:114220600-114235800	Weak transcription	HSMM	muscle
35	chr1:114220600-114237600	Weak transcription	Fetal Heart	heart
36	chr1:114221000-114236000	Weak transcription	A549	lung
37	chr1:114222200-114229600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:114223400-114228400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:114223400-114228400	Strong transcription	Liver	Liver
40	chr1:114224000-114232400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:114224000-114241600	Weak transcription	Left Ventricle	heart
42	chr1:114224600-114231800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:114224600-114232000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:114224600-114232400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:114224600-114236000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:114224800-114230600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:114224800-114232000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:114224800-114237600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:114224800-114237600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:114224800-114238000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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