Variant report

Variant	rs1230673
Chromosome Location	chr1:114194513-114194514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114192533..114195084-chr1:114195478..114197038,2	K562	blood:
2	chr1:114189711..114191330-chr1:114193397..114195766,2	MCF-7	breast:
3	chr1:114186046..114188816-chr1:114192338..114195071,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10776773	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10858006	0.88[ASN][1000 genomes]
rs10858015	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11102667	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102671	0.86[AFR][1000 genomes]
rs11102678	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[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];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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];0.94[ASN][1000 genomes]
rs1146185	0.80[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];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026423	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12138638	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12144309	0.81[GIH][hapmap]
rs1217194	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217202	0.88[ASN][1000 genomes]
rs1217212	0.90[ASN][1000 genomes]
rs1217224	0.90[ASN][1000 genomes]
rs1217225	0.80[ASW][hapmap];0.95[YRI][hapmap]
rs1217229	0.88[ASN][1000 genomes]
rs1217231	0.95[YRI][hapmap]
rs1217238	0.82[ASN][1000 genomes]
rs1217375	0.87[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs1217379	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs1217403	0.85[CHB][hapmap]
rs1230675	0.84[ASN][1000 genomes]
rs1230681	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1230684	0.87[EUR][1000 genomes]
rs1235000	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[ASN][1000 genomes]
rs1237290	0.88[ASN][1000 genomes]
rs12757859	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1343630	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs13524	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]
rs1624335	0.93[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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1743594	0.93[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743595	0.90[ASN][1000 genomes]
rs1777239	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935836	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1970559	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs2040041	1.00[CHD][hapmap];0.94[GIH][hapmap]
rs2185827	0.82[CHB][hapmap]
rs2476599	0.87[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs2476600	0.87[ASW][hapmap];0.82[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797416	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs2798137	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789597	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7518766	0.80[ASN][1000 genomes]
rs7543121	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555634	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs9429525	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	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
3	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
rs1230673	MAGI3	cis	cerebellum	SCAN
rs1230673	RAP1A	cis	parietal	SCAN
rs1230673	PHTF1	cis	parietal	SCAN
rs1230673	AP4B1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114159000-114195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:114159200-114194800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:114161800-114199800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
5	chr1:114173000-114214400	Weak transcription	Esophagus	oesophagus
6	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
7	chr1:114173600-114195000	Weak transcription	HMEC	breast
8	chr1:114173600-114206000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:114173800-114196200	Weak transcription	Gastric	stomach
10	chr1:114173800-114199600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:114173800-114201800	Weak transcription	Colonic Mucosa	Colon
12	chr1:114173800-114201800	Weak transcription	Lung	lung
13	chr1:114173800-114214400	Weak transcription	Pancreas	Pancrea
14	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
16	chr1:114181200-114199400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:114181800-114199800	Weak transcription	Fetal Brain Female	brain
18	chr1:114182000-114219600	Weak transcription	Fetal Kidney	kidney
19	chr1:114182200-114197600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:114182600-114194800	Weak transcription	HSMM	muscle
21	chr1:114182600-114206200	Weak transcription	Hela-S3	cervix
22	chr1:114182800-114201800	Weak transcription	Brain Germinal Matrix	brain
23	chr1:114182800-114201800	Weak transcription	Fetal Brain Male	brain
24	chr1:114182800-114217400	Weak transcription	NHDF-Ad	bronchial
25	chr1:114183000-114196200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:114183000-114200000	Weak transcription	HSMMtube	muscle
27	chr1:114183000-114201200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:114183000-114235800	Weak transcription	Dnd41	blood
29	chr1:114183200-114199600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:114183400-114195400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:114183400-114199800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:114183400-114215800	Weak transcription	Fetal Lung	lung
33	chr1:114183600-114199200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:114183600-114216400	Weak transcription	A549	lung
35	chr1:114184400-114199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:114184600-114204800	Weak transcription	Psoas Muscle	Psoas
37	chr1:114184800-114199800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:114184800-114201800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:114185000-114199600	Weak transcription	Brain Substantia Nigra	brain
40	chr1:114185200-114195000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:114185200-114199400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:114185200-114224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:114185400-114200400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:114185400-114201200	Weak transcription	Brain Angular Gyrus	brain
45	chr1:114185400-114214600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:114185400-114228000	Weak transcription	HepG2	liver
47	chr1:114185800-114223600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:114186600-114195400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:114186800-114200000	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:114187400-114201800	Weak transcription	Primary T cells from cord blood	blood

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