Variant report

Variant	rs11716558
Chromosome Location	chr3:101528481-101528482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101527598..101532607-chr3:101943498..101946338,5	MCF-7	breast:
2	chr3:101525788..101530235-chr3:101566899..101572223,5	K562	blood:
3	chr3:101527800..101528775-chr3:101943010..101944822,8	MCF-7	breast:
4	chr3:101528140..101529807-chr3:101566899..101568797,2	K562	blood:
5	chr3:101527585..101537705-chr3:101566838..101571797,17	MCF-7	breast:
6	chr3:101527637..101528670-chr3:101942662..101943279,3	MCF-7	breast:
7	chr3:101527740..101528670-chr3:101947690..101948436,3	MCF-7	breast:
8	chr3:101527614..101528630-chr3:101943465..101944903,6	MCF-7	breast:
9	chr3:101525154..101528585-chr3:101567591..101569610,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1031710	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706494	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11706986	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11707250	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711903	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712309	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11712888	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714278	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714444	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717046	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717638	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11720745	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11914318	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12631513	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633770	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13059470	0.81[ASN][1000 genomes]
rs13060963	0.83[EUR][1000 genomes]
rs13065944	0.84[EUR][1000 genomes]
rs13066768	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068350	0.84[EUR][1000 genomes]
rs13077925	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13078652	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13084113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13084432	0.83[EUR][1000 genomes]
rs13085776	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13094753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13094911	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13099674	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1460097	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17347156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17347644	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1963961	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1963962	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2318090	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34063583	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34161138	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34181125	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34263427	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34376498	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34648996	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34743741	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34947019	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34963630	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35117343	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35315807	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35799195	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35810977	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35850993	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36002990	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4342086	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58658478	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61396602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62284198	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62284199	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11716558	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101498800-101533800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:101498800-101546200	Weak transcription	Esophagus	oesophagus
3	chr3:101499000-101533000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:101499200-101529600	Weak transcription	Small Intestine	intestine
5	chr3:101502600-101540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:101502600-101540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:101504800-101533600	Weak transcription	Pancreas	Pancrea
8	chr3:101504800-101546000	Weak transcription	Colonic Mucosa	Colon
9	chr3:101505400-101533600	Weak transcription	Right Atrium	heart
10	chr3:101511000-101536000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:101515200-101540200	Weak transcription	NHLF	lung
12	chr3:101515400-101528600	Weak transcription	HMEC	breast
13	chr3:101515400-101535800	Weak transcription	NHEK	skin
14	chr3:101515400-101546000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:101516000-101546000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:101520400-101546000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:101520800-101532000	Weak transcription	Psoas Muscle	Psoas
18	chr3:101520800-101535800	Weak transcription	Aorta	Aorta
19	chr3:101520800-101535800	Weak transcription	Spleen	Spleen
20	chr3:101520800-101536200	Weak transcription	Right Ventricle	heart
21	chr3:101520800-101539600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:101520800-101540200	Weak transcription	Lung	lung
23	chr3:101520800-101546400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:101521000-101531800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:101521000-101532800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:101521000-101533000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:101521000-101535800	Weak transcription	Thymus	Thymus
28	chr3:101521200-101533800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:101521200-101535800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:101521200-101546200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:101521400-101528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:101521400-101535800	Weak transcription	Brain Germinal Matrix	brain
33	chr3:101521400-101535800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:101521400-101536000	Weak transcription	Fetal Brain Female	brain
35	chr3:101522000-101535800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:101522200-101535400	Weak transcription	HSMMtube	muscle
37	chr3:101522200-101540600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:101522800-101532000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:101522800-101532000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:101522800-101535800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:101522800-101535800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:101522800-101535800	Weak transcription	Ovary	ovary
43	chr3:101522800-101536200	Weak transcription	Fetal Stomach	stomach
44	chr3:101522800-101540200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:101523000-101535800	Weak transcription	Fetal Brain Male	brain
46	chr3:101523200-101528800	Weak transcription	Fetal Thymus	thymus
47	chr3:101523200-101533000	Weak transcription	Stomach Mucosa	stomach
48	chr3:101523200-101536200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:101523400-101528800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:101523400-101540400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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