Variant report

Variant	rs1539411
Chromosome Location	chr1:113938988-113938989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113938477..113941904-chr1:113943268..113946445,5	MCF-7	breast:
2	chr1:113762744..113764884-chr1:113937680..113940514,2	MCF-7	breast:
3	chr1:113933530..113935652-chr1:113937378..113940053,4	K562	blood:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10458458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10458459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857994	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11102627	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs11102628	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs11102630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11102636	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11102637	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11102638	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs11102639	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs11102641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11102647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1112085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12021783	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12022849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12023641	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12024428	0.99[ASN][1000 genomes]
rs12026682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12029305	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12030900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034178	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12038473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12038879	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12039603	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12039669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12039944	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs12044485	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12045148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12045559	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12046451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12048327	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12049093	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049447	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12567622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap]
rs1936927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs1936928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2027536	0.97[ASN][1000 genomes]
rs2027537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838987	0.82[AMR][1000 genomes]
rs4838988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap]
rs4839320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839323	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4839324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs55737954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66565865	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6688827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs72687924	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9787276	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
5	esv3411362	chr1:113938903-113939418	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539411	MAGI3	cis	cerebellum	SCAN
rs1539411	CAPZA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113934800-113945200	Weak transcription	Gastric	stomach
2	chr1:113934800-113945200	Weak transcription	Left Ventricle	heart
3	chr1:113935000-113939000	Weak transcription	HSMM	muscle
4	chr1:113935000-113939200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:113935200-113943200	Weak transcription	HUVEC	blood vessel
6	chr1:113935200-113945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:113935200-113949400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:113935400-113939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:113935400-113939200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:113935400-113939600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:113935400-113939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:113935600-113939000	Weak transcription	Osteobl	bone
13	chr1:113935600-113939200	Weak transcription	NH-A	brain
14	chr1:113935600-113939400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:113935600-113939400	Enhancers	Hela-S3	cervix
16	chr1:113935600-113941400	Weak transcription	Fetal Lung	lung
17	chr1:113935600-113941800	Weak transcription	Ovary	ovary
18	chr1:113935600-113949400	Weak transcription	Aorta	Aorta
19	chr1:113936000-113939200	Weak transcription	NHLF	lung
20	chr1:113936000-113945200	Weak transcription	Right Atrium	heart
21	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
22	chr1:113936200-113941400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:113936600-113939200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:113936800-113939400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:113936800-113945200	Weak transcription	Brain Germinal Matrix	brain
26	chr1:113936800-113945200	Weak transcription	Pancreas	Pancrea
27	chr1:113937000-113939000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:113937200-113948200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:113937400-113939000	Weak transcription	NHDF-Ad	bronchial
30	chr1:113937400-113940000	Weak transcription	Fetal Brain Female	brain
31	chr1:113937400-113940600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:113937400-113941600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:113937600-113939400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:113937600-113939600	Enhancers	HepG2	liver
35	chr1:113937600-113940000	Weak transcription	Fetal Brain Male	brain
36	chr1:113937600-113940000	Weak transcription	Fetal Intestine Large	intestine
37	chr1:113937600-113940800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:113937600-113945600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:113937600-113947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:113937800-113939000	Enhancers	A549	lung
42	chr1:113937800-113940200	Enhancers	Liver	Liver
43	chr1:113937800-113946400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:113938000-113939200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:113938000-113946200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:113938800-113939200	Weak transcription	Stomach Mucosa	stomach
47	chr1:113938800-113940000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:113938800-113940000	Enhancers	NHEK	skin
49	chr1:113938800-113940200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:113938800-113940200	Enhancers	HMEC	breast

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