Variant report

Variant	rs2048558
Chromosome Location	chr1:150571730-150571731
allele	C/T
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTSL4-6	chr1:150571618-150571837	l_134_chr1:150571617-150577187_ovary

No data

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1053732	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888384	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888385	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204668	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204669	0.87[ASN][1000 genomes]
rs11204675	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204676	0.81[AFR][1000 genomes]
rs11204677	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204678	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204679	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204680	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204684	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204693	0.83[CHD][hapmap]
rs11204695	0.81[CHD][hapmap]
rs11585169	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116492	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12125672	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126271	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12139563	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406712	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12568757	0.81[CHD][hapmap]
rs12746899	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971378	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738484	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738485	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754209	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970918	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970923	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970924	0.81[CHD][hapmap]
rs4970926	0.81[CHD][hapmap]
rs4971041	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55862611	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61820165	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669122	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6694531	0.81[CHD][hapmap]
rs6697620	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520022	0.81[CHD][hapmap]
rs878471	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs932054	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9803935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[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:30)

SNP	Gene	Cis/trans	Tissue	Source
rs2048558	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs2048558	HORMAD1	cis	Nerve Tibial	GTEx
rs2048558	ARNT	cis	cerebellum	SCAN
rs2048558	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2048558	ARNT	cis	Thyroid	GTEx
rs2048558	HORMAD1	cis	normal skin	skin_eQTL
rs2048558	FMO5	cis	cerebellum	SCAN
rs2048558	HORMAD1	cis	parietal	SCAN
rs2048558	POLR3GL	cis	cerebellum	SCAN
rs2048558	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2048558	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2048558	CTSS	cis	cerebellum	SCAN
rs2048558	CTSS	cis	Nerve Tibial	GTEx
rs2048558	ARNT	cis	normal skin	skin_eQTL
rs2048558	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2048558	TCHHL1	cis	parietal	SCAN
rs2048558	ARNT	cis	parietal	SCAN
rs2048558	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2048558	TXNIP	cis	parietal	SCAN
rs2048558	HORMAD1	cis	uninvolved skin	skin_eQTL
rs2048558	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs2048558	PSMD4	cis	parietal	SCAN
rs2048558	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs2048558	MCL1	cis	cerebellum	SCAN
rs2048558	CTSK	cis	parietal	SCAN
rs2048558	GOLPH3L	cis	Nerve Tibial	GTEx
rs2048558	HORMAD1	cis	lesional skin	skin_eQTL
rs2048558	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2048558	CTSK	cis	cerebellum	SCAN
rs2048558	CTSS	cis	parietal	SCAN

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	chr1:150554000-150572000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:150554400-150572600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:150555400-150572600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
18	chr1:150560200-150576000	Weak transcription	Ovary	ovary
19	chr1:150561200-150572400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:150561400-150577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:150561800-150581800	Weak transcription	Brain Substantia Nigra	brain
22	chr1:150562200-150583200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:150563000-150572400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
25	chr1:150564000-150576200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:150565000-150572600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:150565400-150572000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:150565400-150572600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:150565600-150572600	Weak transcription	Placenta	Placenta
31	chr1:150566200-150571800	Weak transcription	Fetal Stomach	stomach
32	chr1:150566200-150572000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:150566200-150572400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:150566200-150572600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:150566200-150575800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:150566200-150575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:150566200-150576200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:150566400-150572600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:150566400-150575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:150566400-150583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:150566600-150577000	Weak transcription	Aorta	Aorta
42	chr1:150566800-150572600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:150566800-150577000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:150568000-150583000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:150568200-150573400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:150568200-150575400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:150568600-150576600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr1:150568600-150576800	Weak transcription	Spleen	Spleen
49	chr1:150568800-150572600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:150568800-150575400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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