Variant report

Variant	rs11717046
Chromosome Location	chr3:101450258-101450259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:101449575-101450409	PBDE	blood:	n/a	chr3:101449900-101449907 chr3:101449907-101449924

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101442986..101444875-chr3:101449623..101452459,2	K562	blood:
2	chr3:101442812..101446564-chr3:101447514..101451312,4	MCF-7	breast:

Variant related genes	Relation type
CEP97	TF binding region
ENSG00000182504	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1031710	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056579	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1138818	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706494	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706986	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707250	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710533	0.84[EUR][1000 genomes]
rs11710805	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711079	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711903	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712888	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714444	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716558	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717638	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720745	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914318	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917569	0.85[EUR][1000 genomes]
rs11917682	0.85[EUR][1000 genomes]
rs11919389	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11924013	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11925001	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629658	0.85[EUR][1000 genomes]
rs12629954	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12631513	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633089	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633770	0.83[AMR][1000 genomes]
rs12635128	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636557	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639028	0.83[EUR][1000 genomes]
rs13059470	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060963	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065944	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13066768	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13068350	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069443	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077703	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077925	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13078652	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081846	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084113	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084432	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13085776	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094911	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096323	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13099674	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13100262	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1460097	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347156	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17347644	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963961	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963962	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288272	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290859	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303474	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318090	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094295	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094296	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094297	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109756	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34063583	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34263427	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34376498	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34624546	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34648996	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34743741	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34883763	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34947019	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34963630	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35315807	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35799195	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35810977	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35850993	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36002990	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36060163	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806653	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806654	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3864012	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342086	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55654108	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55859364	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56291106	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58658478	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59596156	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61396602	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62284198	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62284199	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768327	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71625262	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628866	0.84[ASN][1000 genomes]
rs7629753	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645391	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651406	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651721	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830943	0.84[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11717046	NXPE3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101444600-101450400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:101444600-101450800	Weak transcription	Lung	lung
3	chr3:101444600-101451000	Weak transcription	Gastric	stomach
4	chr3:101444600-101452800	Weak transcription	Spleen	Spleen
5	chr3:101444600-101453200	Weak transcription	Pancreas	Pancrea
6	chr3:101444600-101454800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:101444800-101450400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:101444800-101451000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:101444800-101451000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:101444800-101451000	Weak transcription	Esophagus	oesophagus
11	chr3:101444800-101451000	Weak transcription	Psoas Muscle	Psoas
12	chr3:101444800-101453400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:101444800-101454200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:101445000-101450400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:101445000-101450600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:101445000-101450800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:101445000-101450800	Weak transcription	Aorta	Aorta
18	chr3:101445000-101450800	Weak transcription	Liver	Liver
19	chr3:101445000-101450800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:101445000-101451000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:101445000-101451000	Weak transcription	Colonic Mucosa	Colon
22	chr3:101445000-101451200	Weak transcription	Small Intestine	intestine
23	chr3:101445000-101453000	Weak transcription	Stomach Mucosa	stomach
24	chr3:101445000-101453200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:101445200-101450800	Weak transcription	Adipose Nuclei	Adipose
26	chr3:101445200-101450800	Weak transcription	Fetal Kidney	kidney
27	chr3:101445200-101452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:101445200-101453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:101445400-101453000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:101445400-101455600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:101445400-101455600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:101445600-101452400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:101445600-101454600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:101445600-101456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
36	chr3:101445800-101450600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:101445800-101452800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:101445800-101453400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:101445800-101454200	Strong transcription	HSMM	muscle
40	chr3:101445800-101454400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:101445800-101454600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:101445800-101454800	Strong transcription	Fetal Thymus	thymus
43	chr3:101445800-101456200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:101445800-101456200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:101446200-101451200	Strong transcription	Fetal Brain Female	brain
46	chr3:101446200-101454200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:101446200-101454200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:101446200-101454200	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:101446200-101455600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:101446200-101455600	Strong transcription	Thymus	Thymus

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