Variant report

Variant	rs12778199
Chromosome Location	chr10:89551106-89551107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10082347	0.93[EUR][1000 genomes]
rs1051441	0.96[EUR][1000 genomes]
rs10887753	0.97[EUR][1000 genomes]
rs11202531	0.81[EUR][1000 genomes]
rs11202536	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11202538	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11202553	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11202557	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11202563	0.97[EUR][1000 genomes]
rs11202564	0.87[CEU][hapmap]
rs11202565	0.92[EUR][1000 genomes]
rs11202568	0.95[EUR][1000 genomes]
rs11202571	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11498630	0.97[EUR][1000 genomes]
rs11812787	0.98[EUR][1000 genomes]
rs11816798	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11817759	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11818430	1.00[EUR][1000 genomes]
rs12247482	1.00[EUR][1000 genomes]
rs12253113	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12413371	0.95[EUR][1000 genomes]
rs12570131	0.97[EUR][1000 genomes]
rs12570639	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12571331	0.85[EUR][1000 genomes]
rs12572346	0.89[EUR][1000 genomes]
rs12572581	0.91[EUR][1000 genomes]
rs12573160	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12573349	1.00[EUR][1000 genomes]
rs12762731	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12764439	0.80[EUR][1000 genomes]
rs12765184	0.96[EUR][1000 genomes]
rs12765681	0.99[EUR][1000 genomes]
rs12768487	0.96[EUR][1000 genomes]
rs12769214	0.98[EUR][1000 genomes]
rs12769771	0.92[EUR][1000 genomes]
rs12770433	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12770684	1.00[EUR][1000 genomes]
rs12771188	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12771844	0.97[EUR][1000 genomes]
rs12772552	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12773536	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12775017	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12775041	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12776656	0.96[EUR][1000 genomes]
rs12779667	0.94[EUR][1000 genomes]
rs12779915	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12780234	0.93[EUR][1000 genomes]
rs12780237	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12781171	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12782128	0.96[EUR][1000 genomes]
rs12782235	1.00[EUR][1000 genomes]
rs12782454	0.99[EUR][1000 genomes]
rs12783598	0.89[CEU][hapmap];1.00[EUR][1000 genomes]
rs17096702	0.92[EUR][1000 genomes]
rs1819162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819163	1.00[EUR][1000 genomes]
rs1853167	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1923260	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs1923261	1.00[EUR][1000 genomes]
rs1923262	0.91[CEU][hapmap];1.00[EUR][1000 genomes]
rs1960047	0.96[EUR][1000 genomes]
rs1993845	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs2038554	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2057358	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2067661	0.94[EUR][1000 genomes]
rs2306157	0.92[EUR][1000 genomes]
rs34325090	0.96[EUR][1000 genomes]
rs34466534	0.96[EUR][1000 genomes]
rs34559481	0.96[EUR][1000 genomes]
rs34878240	0.96[EUR][1000 genomes]
rs35254974	0.96[EUR][1000 genomes]
rs35388513	0.85[EUR][1000 genomes]
rs35662941	0.88[EUR][1000 genomes]
rs35814940	0.85[EUR][1000 genomes]
rs3740278	0.93[EUR][1000 genomes]
rs3815417	1.00[YRI][hapmap]
rs3816651	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4443987	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6586102	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs66863455	0.96[EUR][1000 genomes]
rs7068497	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7073644	0.95[EUR][1000 genomes]
rs7090088	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7090432	0.95[EUR][1000 genomes]
rs7096449	0.96[EUR][1000 genomes]
rs7098653	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs7480	0.96[EUR][1000 genomes]
rs7481	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.85[EUR][1000 genomes]
rs7904344	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7905932	0.94[EUR][1000 genomes]
rs7908203	0.96[EUR][1000 genomes]
rs7910692	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7913763	0.87[EUR][1000 genomes]
rs7920778	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7920910	0.94[EUR][1000 genomes]
rs7921889	0.94[EUR][1000 genomes]
rs9651491	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9663978	1.00[EUR][1000 genomes]
rs9664653	1.00[CEU][hapmap];1.00[EUR][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
rs12778199	ATAD1	cis	lung	GTEx

Chromatin state (count:124 , 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	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
6	chr10:89507000-89557600	Weak transcription	Lung	lung
7	chr10:89510200-89553800	Weak transcription	Esophagus	oesophagus
8	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
9	chr10:89512800-89560400	Weak transcription	Fetal Brain Male	brain
10	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:89516400-89557800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:89518200-89556600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:89518400-89559000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr10:89520400-89556400	Weak transcription	Brain Germinal Matrix	brain
15	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
16	chr10:89523200-89553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:89523400-89562800	Weak transcription	K562	blood
18	chr10:89523800-89562000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr10:89524600-89560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:89527400-89553600	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:89527600-89554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:89527600-89554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:89536200-89557800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr10:89536200-89574600	Weak transcription	Brain Anterior Caudate	brain
27	chr10:89537000-89560400	Weak transcription	Small Intestine	intestine
28	chr10:89537000-89576400	Weak transcription	HSMMtube	muscle
29	chr10:89538000-89552800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr10:89538200-89558600	Strong transcription	Hela-S3	cervix
31	chr10:89538800-89556600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:89540000-89556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:89540200-89551800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr10:89540200-89560000	Weak transcription	Fetal Kidney	kidney
35	chr10:89540200-89562800	Weak transcription	Fetal Heart	heart
36	chr10:89540800-89560000	Weak transcription	Fetal Brain Female	brain
37	chr10:89540800-89563000	Weak transcription	Ovary	ovary
38	chr10:89541800-89575000	Weak transcription	Right Ventricle	heart
39	chr10:89542000-89571200	Weak transcription	Brain Hippocampus Middle	brain
40	chr10:89542800-89556200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr10:89543000-89556600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:89543000-89562000	Weak transcription	Thymus	Thymus
43	chr10:89543000-89571400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr10:89543200-89551200	Weak transcription	NHDF-Ad	bronchial
45	chr10:89543200-89551800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:89543200-89554200	Weak transcription	Pancreas	Pancrea
47	chr10:89543200-89556200	Weak transcription	Fetal Stomach	stomach
48	chr10:89543200-89557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:89543200-89559000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr10:89543200-89563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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