Variant report

Variant	rs13061565
Chromosome Location	chr3:101392270-101392271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101388186..101389836-chr3:101391402..101393014,2	K562	blood:
2	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
3	chr3:101391957..101394072-chr3:101395408..101397212,3	MCF-7	breast:
4	chr3:101292143..101294158-chr3:101391089..101392992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081154	Chromatin interaction
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1031710	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.95[AFR][1000 genomes];1.00[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	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712748	0.91[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	0.90[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	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923273	0.83[AMR][1000 genomes]
rs11924013	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635128	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13065944	0.86[ASN][1000 genomes]
rs13066768	0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17411983	0.93[AFR][1000 genomes];1.00[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	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303474	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094296	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.91[ASN][1000 genomes]
rs34624546	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.93[AFR][1000 genomes];0.97[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	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55654108	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59596156	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62284162	0.83[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.81[AFR][1000 genomes];0.92[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
rs13061565	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs13061565	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 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	chr3:101373200-101393800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:101373200-101394000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:101374200-101394600	Weak transcription	Esophagus	oesophagus
7	chr3:101380600-101393000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:101382600-101392800	Weak transcription	Gastric	stomach
9	chr3:101382600-101393800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:101383000-101395000	Weak transcription	Spleen	Spleen
11	chr3:101383400-101394000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:101383400-101394200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:101383600-101394800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:101384400-101393800	Weak transcription	Fetal Heart	heart
15	chr3:101384400-101393800	Weak transcription	Right Ventricle	heart
16	chr3:101384400-101394000	Weak transcription	Brain Germinal Matrix	brain
17	chr3:101384600-101394000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:101384600-101394000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:101384600-101394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:101384600-101394400	Weak transcription	HSMMtube	muscle
21	chr3:101384800-101394400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:101385000-101394400	Weak transcription	Lung	lung
23	chr3:101385400-101393800	Weak transcription	NHLF	lung
24	chr3:101386200-101393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:101386200-101393000	Weak transcription	Pancreas	Pancrea
26	chr3:101386200-101393600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:101386200-101394400	Weak transcription	Ovary	ovary
28	chr3:101386400-101394200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:101386600-101394400	Weak transcription	Psoas Muscle	Psoas
30	chr3:101387400-101393800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:101387400-101394000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:101387600-101393800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:101388200-101394600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:101388600-101394400	Weak transcription	Colonic Mucosa	Colon
35	chr3:101388800-101394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:101389000-101394400	Weak transcription	Fetal Stomach	stomach
37	chr3:101389800-101394400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:101389800-101394400	Weak transcription	Fetal Intestine Small	intestine
39	chr3:101390000-101393800	Weak transcription	HUVEC	blood vessel
40	chr3:101390200-101393000	Weak transcription	Fetal Brain Male	brain
41	chr3:101390200-101393400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:101390200-101393600	Weak transcription	Fetal Intestine Large	intestine
43	chr3:101390200-101393800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:101390200-101393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:101390200-101394000	Weak transcription	NH-A	brain
46	chr3:101390200-101394200	Weak transcription	Fetal Kidney	kidney
47	chr3:101390200-101394600	Weak transcription	Aorta	Aorta
48	chr3:101390400-101392400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:101390400-101393000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:101390400-101393000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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