Variant report

Variant	rs12782454
Chromosome Location	chr10:89558469-89558470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89557779..89559626-chr10:89565125..89566841,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10082347	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1051441	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10887753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202531	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11202536	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11202538	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11202553	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202557	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202564	0.81[AMR][1000 genomes]
rs11202565	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202568	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11202571	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11498630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812787	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11816798	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11817759	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11818430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12247482	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12253113	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12413371	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12570131	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570639	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571331	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12572346	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12572581	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573160	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12573349	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12762731	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12765184	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12765681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12768487	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12769214	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12769771	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770433	0.91[EUR][1000 genomes]
rs12770684	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12771188	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12771844	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772552	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773536	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775017	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775041	0.95[EUR][1000 genomes]
rs12776656	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12778199	0.99[EUR][1000 genomes]
rs12779667	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779915	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780234	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12780237	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781171	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782128	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12782235	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12783598	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096702	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819162	0.99[EUR][1000 genomes]
rs1819163	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853167	0.81[AMR][1000 genomes]
rs1923260	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923261	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923262	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1960047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993845	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2038554	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057358	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2067661	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306157	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34325090	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34466534	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34559481	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34878240	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35254974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35388513	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35662941	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35814940	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3740278	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3816651	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4443987	0.95[EUR][1000 genomes]
rs6586102	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66863455	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7073644	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7085412	0.81[AMR][1000 genomes]
rs7090088	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090432	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7096449	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7098653	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7480	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7481	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7898915	0.81[AMR][1000 genomes]
rs7901767	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7904344	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7905932	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7908203	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7910692	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7913763	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7920778	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7920910	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921889	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9651491	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9663978	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9664653	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12782454	ATAD1	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89473000-89577200	Weak transcription	Gastric	stomach
2	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
5	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
6	chr10:89512800-89560400	Weak transcription	Fetal Brain Male	brain
7	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:89518400-89559000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
10	chr10:89523400-89562800	Weak transcription	K562	blood
11	chr10:89523800-89562000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:89524600-89560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:89536200-89574600	Weak transcription	Brain Anterior Caudate	brain
16	chr10:89537000-89560400	Weak transcription	Small Intestine	intestine
17	chr10:89537000-89576400	Weak transcription	HSMMtube	muscle
18	chr10:89538200-89558600	Strong transcription	Hela-S3	cervix
19	chr10:89540200-89560000	Weak transcription	Fetal Kidney	kidney
20	chr10:89540200-89562800	Weak transcription	Fetal Heart	heart
21	chr10:89540800-89560000	Weak transcription	Fetal Brain Female	brain
22	chr10:89540800-89563000	Weak transcription	Ovary	ovary
23	chr10:89541800-89575000	Weak transcription	Right Ventricle	heart
24	chr10:89542000-89571200	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:89543000-89562000	Weak transcription	Thymus	Thymus
26	chr10:89543000-89571400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:89543200-89559000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:89543200-89563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:89543200-89572200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:89543400-89577200	Weak transcription	Aorta	Aorta
31	chr10:89546000-89559200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:89547000-89563800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:89548200-89574800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:89549400-89575400	Weak transcription	Brain Angular Gyrus	brain
35	chr10:89549600-89559000	Weak transcription	Fetal Intestine Small	intestine
36	chr10:89549800-89561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:89550000-89572200	Weak transcription	HUVEC	blood vessel
38	chr10:89551200-89560000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr10:89552400-89559000	Weak transcription	NHLF	lung
40	chr10:89552400-89560600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr10:89552400-89562000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:89552600-89566200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:89552800-89562000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:89552800-89571400	Weak transcription	NHEK	skin
45	chr10:89553000-89560400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:89553000-89570000	Weak transcription	HMEC	breast
47	chr10:89553200-89565800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr10:89553200-89569800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr10:89553600-89559200	Weak transcription	HepG2	liver
50	chr10:89553800-89560000	Weak transcription	A549	lung

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