Variant report

Variant	rs1077526
Chromosome Location	chr4:106347156-106347157
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	chr4:106340779..106343973-chr4:106344387..106347372,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1126066	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.83[EUR][1000 genomes]
rs17035550	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	1.00[ASN][1000 genomes]
rs17035619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509136	1.00[ASN][1000 genomes]
rs1874758	0.82[CEU][hapmap]
rs2004290	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898404	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41438151	0.89[MEX][hapmap]
rs4499701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902936	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533194	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517713	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66763438	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67476913	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829168	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.84[EUR][1000 genomes]
rs72668208	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1077526	SGMS2	cis	cerebellum	SCAN
rs1077526	BANK1	cis	parietal	SCAN
rs1077526	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
5	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
7	chr4:106321600-106356200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:106321800-106353600	Weak transcription	HMEC	breast
9	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
10	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:106326200-106347600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:106327200-106365200	Weak transcription	Osteobl	bone
15	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
16	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:106330400-106347200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:106330600-106356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:106334800-106347600	Weak transcription	A549	lung
20	chr4:106336400-106347600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:106336400-106347600	Weak transcription	NHEK	skin
22	chr4:106336600-106356400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:106336800-106347400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:106336800-106347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:106336800-106347400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:106336800-106347400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:106336800-106347400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:106336800-106347400	Weak transcription	Colonic Mucosa	Colon
29	chr4:106336800-106347400	Weak transcription	Lung	lung
30	chr4:106336800-106347400	Weak transcription	Pancreas	Pancrea
31	chr4:106336800-106347400	Weak transcription	Spleen	Spleen
32	chr4:106336800-106347600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
34	chr4:106336800-106387800	Weak transcription	NHLF	lung
35	chr4:106337000-106347400	Weak transcription	Aorta	Aorta
36	chr4:106337000-106347400	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:106337000-106347400	Weak transcription	Esophagus	oesophagus
38	chr4:106337000-106347400	Weak transcription	Gastric	stomach
39	chr4:106337000-106347400	Weak transcription	Thymus	Thymus
40	chr4:106337000-106354400	Weak transcription	Left Ventricle	heart
41	chr4:106337000-106354600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:106337200-106356600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:106338000-106347600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:106338600-106347400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr4:106338800-106347400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:106338800-106347400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:106339200-106347400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr4:106340200-106347400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:106340200-106347600	Weak transcription	Brain Angular Gyrus	brain
50	chr4:106340200-106387800	Weak transcription	H9 Cell Line	embryonic stem cell

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