Variant report

Variant	rs59596156
Chromosome Location	chr3:101394217-101394218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:101394167-101394332	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101306571..101308264-chr3:101393626..101395176,2	MCF-7	breast:
2	chr3:101394090..101397025-chr3:101443461..101445928,3	K562	blood:
3	chr3:101291780..101294720-chr3:101394004..101396565,4	K562	blood:
4	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
5	chr3:101291104..101295547-chr3:101393750..101397705,12	MCF-7	breast:
6	chr3:101293308..101296113-chr3:101394030..101397396,3	MCF-7	breast:
7	chr3:101289588..101293101-chr3:101394155..101396875,5	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB11-AS1	TF binding region
ENSG00000081154	Chromatin interaction
ENSG00000242299	Chromatin interaction
ENSG00000182504	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1031710	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710533	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712748	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717046	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720745	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11924013	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635128	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	0.86[ASN][1000 genomes]
rs13066768	0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.85[EUR][1000 genomes]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17411983	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303474	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094296	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.91[ASN][1000 genomes]
rs34624546	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806653	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55654108	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.81[ASN][1000 genomes]
rs62284162	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59596156	NXPE3	cis	Esophagus Muscularis	GTEx
rs59596156	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:101371000-101394800	Weak transcription	Small Intestine	intestine
4	chr3:101374200-101394600	Weak transcription	Esophagus	oesophagus
5	chr3:101383000-101395000	Weak transcription	Spleen	Spleen
6	chr3:101383600-101394800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:101384600-101394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:101384600-101394400	Weak transcription	HSMMtube	muscle
9	chr3:101384800-101394400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:101385000-101394400	Weak transcription	Lung	lung
11	chr3:101386200-101394400	Weak transcription	Ovary	ovary
12	chr3:101386600-101394400	Weak transcription	Psoas Muscle	Psoas
13	chr3:101388200-101394600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:101388600-101394400	Weak transcription	Colonic Mucosa	Colon
15	chr3:101388800-101394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:101389000-101394400	Weak transcription	Fetal Stomach	stomach
17	chr3:101389800-101394400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:101389800-101394400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:101390200-101394600	Weak transcription	Aorta	Aorta
20	chr3:101390400-101394400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:101390400-101394400	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:101390600-101394400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:101391000-101394400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:101391000-101394400	Weak transcription	Fetal Thymus	thymus
25	chr3:101392400-101394400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:101392600-101394400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:101392800-101394400	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:101392800-101394400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:101393000-101394400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:101393000-101394400	Enhancers	Fetal Brain Male	brain
31	chr3:101393000-101394400	Enhancers	Pancreas	Pancrea
32	chr3:101393000-101394600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:101393200-101394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:101393200-101394400	Enhancers	Placenta	Placenta
35	chr3:101393200-101397600	Active TSS	K562	blood
36	chr3:101393400-101394400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:101393600-101394400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:101393600-101394400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:101393600-101396800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:101393800-101394400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:101393800-101394400	Enhancers	Liver	Liver
42	chr3:101393800-101394400	Enhancers	Brain Angular Gyrus	brain
43	chr3:101393800-101394400	Enhancers	Fetal Heart	heart
44	chr3:101393800-101394400	Enhancers	Fetal Lung	lung
45	chr3:101393800-101394400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:101393800-101394400	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:101393800-101394400	Enhancers	Stomach Mucosa	stomach
48	chr3:101393800-101394400	Flanking Active TSS	HepG2	liver
49	chr3:101393800-101394600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:101393800-101394600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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