Variant report

Variant	rs12139563
Chromosome Location	chr1:150578241-150578242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150549850..150554291-chr1:150574089..150582135,21	MCF-7	breast:
2	chr1:150575837..150580445-chr1:150580466..150584080,8	K562	blood:
3	chr1:150575951..150578868-chr1:150979461..150981036,2	MCF-7	breast:
4	chr1:150575672..150578383-chr1:150583826..150586849,3	MCF-7	breast:
5	chr1:150567222..150571077-chr1:150576959..150580795,4	K562	blood:
6	chr1:150575837..150579446-chr1:150579554..150584365,8	K562	blood:
7	chr1:150569191..150572175-chr1:150574957..150578897,3	K562	blood:
8	chr1:150532872..150535216-chr1:150575745..150578674,3	MCF-7	breast:
9	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
10	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
11	chr1:150575574..150579805-chr1:150584520..150587966,8	K562	blood:
12	chr1:150539586..150542083-chr1:150577790..150580612,2	MCF-7	breast:
13	chr1:150575575..150579360-chr1:150586267..150590184,5	MCF-7	breast:
14	chr1:150562742..150565276-chr1:150576021..150578249,2	K562	blood:
15	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:
16	chr1:150562735..150566350-chr1:150574658..150578740,6	K562	blood:
17	chr1:150547928..150550276-chr1:150576604..150578883,3	K562	blood:
18	chr1:150577398..150579449-chr1:150601432..150603396,2	MCF-7	breast:
19	chr1:150550711..150554920-chr1:150576737..150579310,4	K562	blood:
20	chr1:150550625..150555409-chr1:150574818..150579409,12	K562	blood:
21	chr1:150532467..150535683-chr1:150575722..150579227,4	MCF-7	breast:
22	chr1:150577464..150579256-chr1:150597342..150598945,2	K562	blood:
23	chr1:150533566..150535178-chr1:150577243..150578878,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203804	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1053732	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888384	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888385	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204668	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11204669	0.89[ASN][1000 genomes]
rs11204675	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204677	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204678	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204679	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204680	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204684	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11585169	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12125672	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12126271	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12406712	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12746899	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971378	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048558	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738484	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738485	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754209	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970918	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970923	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971041	0.84[ASN][1000 genomes]
rs55862611	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61820165	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669122	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697620	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698495	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878471	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs932054	0.83[ASN][1000 genomes]
rs9803935	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv946384	chr1:150567346-150579087	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12139563	HORMAD1	cis	Nerve Tibial	GTEx
rs12139563	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12139563	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs12139563	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12139563	GOLPH3L	cis	Nerve Tibial	GTEx
rs12139563	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12139563	RP11-316M1.12	cis	Whole Blood	GTEx
rs12139563	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12139563	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12139563	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12139563	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12139563	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12139563	ENSA	Cis_1M	lymphoblastoid	RTeQTL
rs12139563	ARNT	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:150553200-150581800	Weak transcription	Dnd41	blood
4	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
6	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
8	chr1:150561800-150581800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:150562200-150583200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
11	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:150566400-150583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:150568000-150583000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:150569200-150582200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:150569200-150582200	Weak transcription	GM12878-XiMat	blood
16	chr1:150570400-150582200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:150571000-150583800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:150572800-150581800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:150573200-150583000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:150573400-150581600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:150573400-150581800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:150573400-150582000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:150573400-150582200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:150573400-150582200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:150573400-150582200	Weak transcription	Brain Angular Gyrus	brain
26	chr1:150573400-150583000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:150573400-150583200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:150573400-150583400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:150573400-150583600	Weak transcription	Colonic Mucosa	Colon
30	chr1:150573400-150584200	Weak transcription	Thymus	Thymus
31	chr1:150573400-150587800	Weak transcription	Brain Germinal Matrix	brain
32	chr1:150573600-150578800	Weak transcription	Fetal Thymus	thymus
33	chr1:150573600-150583800	Weak transcription	Fetal Brain Female	brain
34	chr1:150573600-150583800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:150575400-150583400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:150576200-150579800	Weak transcription	Fetal Stomach	stomach
37	chr1:150576200-150581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:150576200-150591000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:150576400-150582200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:150577000-150588400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:150577200-150579200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr1:150577200-150581800	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:150577400-150578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:150577400-150581600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:150577400-150581800	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:150577400-150581800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:150577400-150581800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:150577400-150585800	Weak transcription	Aorta	Aorta
49	chr1:150577400-150587800	Weak transcription	Esophagus	oesophagus
50	chr1:150577600-150579400	Enhancers	K562	blood

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