Variant report

Variant	rs11072403
Chromosome Location	chr15:73426298-73426299
allele	A/G
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	MYC	chr15:73426263-73426352	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:73426284-73426389	K562	blood:	n/a	n/a

Variant related genes	Relation type
NEO1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1023924	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1038137	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10467948	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072406	0.81[ASN][1000 genomes]
rs1116880	0.85[ASN][1000 genomes]
rs12050774	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902768	0.82[ASN][1000 genomes]
rs13379875	0.81[AMR][1000 genomes]
rs1479338	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1479339	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17762146	0.86[EUR][1000 genomes]
rs17762516	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17762600	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17829830	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17829957	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1812835	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1871385	0.81[ASN][1000 genomes]
rs1964543	0.87[EUR][1000 genomes]
rs2169951	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2415148	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3985588	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4132536	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4545783	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4609810	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776624	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776625	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4777590	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55646651	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55836604	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55868723	0.85[ASN][1000 genomes]
rs55925663	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55939596	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56215298	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56269104	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56348595	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56377702	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59066156	0.88[ASN][1000 genomes]
rs62016797	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62016803	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62016805	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62016806	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016808	0.87[EUR][1000 genomes]
rs62016809	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016813	0.87[EUR][1000 genomes]
rs62016814	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016849	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016851	0.91[ASN][1000 genomes]
rs62016853	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62016854	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62017774	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62017776	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165610	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74022925	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025262	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747872	0.81[ASN][1000 genomes]
rs747873	0.81[ASN][1000 genomes]
rs8024575	0.81[ASN][1000 genomes]
rs8026121	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8042700	0.81[ASN][1000 genomes]
rs9806496	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9972347	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11072403	NEO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73388800-73431200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
3	chr15:73400400-73434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:73401200-73428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
6	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
7	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
8	chr15:73406600-73432600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:73407400-73431600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:73408000-73443400	Weak transcription	Adipose Nuclei	Adipose
11	chr15:73409200-73429200	Weak transcription	Esophagus	oesophagus
12	chr15:73410600-73434600	Weak transcription	Liver	Liver
13	chr15:73410800-73431400	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:73413200-73437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:73413400-73434200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:73413600-73446400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:73414000-73428200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:73414000-73437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:73414000-73440000	Weak transcription	Fetal Brain Female	brain
20	chr15:73414200-73428600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:73414200-73445600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
23	chr15:73414600-73436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:73415400-73446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:73415600-73428400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:73416600-73428400	Weak transcription	Fetal Lung	lung
28	chr15:73416600-73444600	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:73416600-73444600	Weak transcription	Lung	lung
30	chr15:73416800-73448800	Weak transcription	Ovary	ovary
31	chr15:73417000-73443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:73418200-73433200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:73418600-73430600	Weak transcription	Fetal Brain Male	brain
34	chr15:73419400-73428800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:73420600-73434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:73421000-73443200	Weak transcription	Brain Angular Gyrus	brain
37	chr15:73421400-73433600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:73423400-73428800	Weak transcription	Fetal Intestine Large	intestine
39	chr15:73423400-73429000	Weak transcription	Aorta	Aorta
40	chr15:73423400-73429200	Weak transcription	Fetal Intestine Small	intestine
41	chr15:73423400-73431200	Weak transcription	Fetal Stomach	stomach
42	chr15:73423400-73438200	Weak transcription	Brain Anterior Caudate	brain
43	chr15:73423400-73445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:73423400-73448800	Weak transcription	Pancreas	Pancrea
45	chr15:73423600-73427600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:73423600-73429000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:73423600-73443200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:73423600-73444600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:73424000-73433600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:73424200-73428800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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