Variant report

Variant	rs1819162
Chromosome Location	chr10:89527210-89527211
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89526081..89527597-chr10:89531587..89533299,2	K562	blood:
2	chr10:89526077..89527625-chr10:89531799..89535725,3	K562	blood:
3	chr10:89522883..89524581-chr10:89525481..89528269,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

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];0.94[CHD][hapmap];1.00[TSI][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];0.94[CHD][hapmap];1.00[TSI][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];1.00[TSI][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];0.94[CHD][hapmap];1.00[TSI][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	1.00[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];0.89[CHD][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12775041	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12776656	0.96[EUR][1000 genomes]
rs12778199	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]
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];0.94[CHD][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12781171	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[TSI][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]
rs1819163	1.00[EUR][1000 genomes]
rs1853167	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1923260	1.00[EUR][1000 genomes]
rs1923261	1.00[EUR][1000 genomes]
rs1923262	0.91[CEU][hapmap];0.89[CHD][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes]
rs1960047	0.96[EUR][1000 genomes]
rs1993845	1.00[CEU][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2038554	0.95[CEU][hapmap];0.94[CHD][hapmap];0.89[TSI][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	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6586102	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs66863455	0.96[EUR][1000 genomes]
rs7068497	0.87[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];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.85[EUR][1000 genomes]
rs7904344	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7905932	0.94[EUR][1000 genomes]
rs7908203	0.96[EUR][1000 genomes]
rs7910692	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7913763	0.87[EUR][1000 genomes]
rs7920778	1.00[CEU][hapmap];0.92[TSI][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];0.94[CHD][hapmap];1.00[TSI][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1819162	ATAD1	cis	lung	GTEx
rs1819162	PAPSS2	cis	lymphoblastoid	seeQTL
rs1819162	LIPJ	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89463000-89541400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:89473000-89577200	Weak transcription	Gastric	stomach
3	chr10:89476200-89542400	Weak transcription	Pancreas	Pancrea
4	chr10:89495000-89541400	Weak transcription	Right Ventricle	heart
5	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:89495200-89530600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:89495200-89542600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:89495200-89544600	Weak transcription	Brain Substantia Nigra	brain
9	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
11	chr10:89498200-89541400	Weak transcription	Aorta	Aorta
12	chr10:89498800-89536200	Weak transcription	Small Intestine	intestine
13	chr10:89503400-89528400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
15	chr10:89507000-89557600	Weak transcription	Lung	lung
16	chr10:89510200-89553800	Weak transcription	Esophagus	oesophagus
17	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
18	chr10:89512800-89560400	Weak transcription	Fetal Brain Male	brain
19	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr10:89514600-89528600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:89514600-89534600	Weak transcription	Ovary	ovary
22	chr10:89514600-89539800	Weak transcription	Fetal Kidney	kidney
23	chr10:89516000-89541200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:89516200-89535400	Weak transcription	Brain Anterior Caudate	brain
25	chr10:89516400-89528400	Weak transcription	Adipose Nuclei	Adipose
26	chr10:89516400-89541400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:89516400-89557800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr10:89518200-89556600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:89518400-89559000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:89519000-89530800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr10:89520200-89542800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:89520400-89535600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:89520400-89556400	Weak transcription	Brain Germinal Matrix	brain
34	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
35	chr10:89520800-89529000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:89521800-89540400	Weak transcription	Thymus	Thymus
37	chr10:89522200-89535200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr10:89522400-89528200	Weak transcription	NHEK	skin
39	chr10:89522400-89535400	Weak transcription	NHLF	lung
40	chr10:89522600-89530400	Strong transcription	GM12878-XiMat	blood
41	chr10:89522600-89530800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr10:89523000-89528400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:89523000-89530400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:89523000-89530600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:89523000-89530600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr10:89523000-89530800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr10:89523000-89530800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:89523000-89531000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:89523000-89531400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:89523200-89527400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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