Variant report

Variant	rs11585169
Chromosome Location	chr1:150572037-150572038
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150548916..150554244-chr1:150567107..150572261,6	K562	blood:
2	chr1:150551177..150554624-chr1:150569491..150572047,3	K562	blood:
3	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
4	chr1:150569191..150572175-chr1:150574957..150578897,3	K562	blood:
5	chr1:150545388..150547945-chr1:150570621..150572716,2	K562	blood:
6	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1053732	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888384	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888385	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204668	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11204669	0.87[ASN][1000 genomes]
rs11204675	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204676	0.83[AFR][1000 genomes]
rs11204677	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204678	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204679	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204680	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204684	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12116492	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12125672	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126271	0.90[ASN][1000 genomes]
rs12139563	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12406712	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12746899	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971378	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048558	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738484	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738485	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754209	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970918	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970923	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971041	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55862611	0.91[ASN][1000 genomes]
rs61820165	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669122	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697620	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698495	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878471	0.92[ASN][1000 genomes]
rs932054	0.85[ASN][1000 genomes]
rs9803935	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS 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	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11585169	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11585169	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11585169	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11585169	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11585169	HORMAD1	cis	Nerve Tibial	GTEx
rs11585169	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11585169	ARNT	cis	Thyroid	GTEx
rs11585169	GOLPH3L	cis	Nerve Tibial	GTEx
rs11585169	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11585169	RP11-363I22.3	cis	Whole Blood	GTEx
rs11585169	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
2	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:150553200-150572600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:150553200-150572600	Weak transcription	Fetal Brain Female	brain
5	chr1:150553200-150572800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:150553200-150581800	Weak transcription	Dnd41	blood
9	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
11	chr1:150553800-150572600	Weak transcription	Lung	lung
12	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:150554400-150572600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:150555400-150572600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:150560200-150576000	Weak transcription	Ovary	ovary
18	chr1:150561200-150572400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:150561400-150577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:150561800-150581800	Weak transcription	Brain Substantia Nigra	brain
21	chr1:150562200-150583200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:150563000-150572400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
24	chr1:150564000-150576200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:150565000-150572600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:150565400-150572600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:150565600-150572600	Weak transcription	Placenta	Placenta
29	chr1:150566200-150572400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:150566200-150572600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:150566200-150575800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:150566200-150575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:150566200-150576200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:150566400-150572600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:150566400-150575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:150566400-150583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:150566600-150577000	Weak transcription	Aorta	Aorta
38	chr1:150566800-150572600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:150566800-150577000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:150568000-150583000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:150568200-150573400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:150568200-150575400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:150568600-150576600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:150568600-150576800	Weak transcription	Spleen	Spleen
45	chr1:150568800-150572600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:150568800-150575400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:150568800-150575800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:150568800-150575800	Weak transcription	Pancreas	Pancrea
49	chr1:150568800-150576200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:150568800-150576800	Weak transcription	Adipose Nuclei	Adipose

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