Variant report

Variant	rs1053732
Chromosome Location	chr1:150597890-150597891
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150595731..150598614-chr1:150617206..150619225,2	K562	blood:
2	chr1:150597869..150600331-chr1:150897965..150900367,2	MCF-7	breast:
3	chr1:150548506..150553393-chr1:150590797..150599175,18	MCF-7	breast:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:
6	chr1:150577464..150579256-chr1:150597342..150598945,2	K562	blood:
7	chr1:150595731..150598614-chr1:150616127..150619225,3	K562	blood:
8	chr1:150596818..150598421-chr1:150785582..150787541,2	MCF-7	breast:
9	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
10	chr1:150548467..150555490-chr1:150590800..150598161,17	MCF-7	breast:
11	chr1:150544073..150554289-chr1:150582699..150598712,61	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ENSA-1	chr1:150597676-150598164	NONHSAT006320

No data

Variant related genes	Relation type
ENSG00000203804	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000264508	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10888384	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888385	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204668	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11204669	0.80[ASN][1000 genomes]
rs11204675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204677	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204678	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204679	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204693	0.86[YRI][hapmap]
rs11204695	0.86[YRI][hapmap]
rs11585169	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12116492	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs12125672	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126271	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12139563	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406712	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12568757	0.86[YRI][hapmap]
rs12746899	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1971378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048558	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]
rs3738484	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738485	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754209	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970918	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970924	0.86[YRI][hapmap]
rs4970926	0.86[YRI][hapmap]
rs4971041	0.82[CEU][hapmap];0.84[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs55862611	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61820165	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669122	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694531	0.86[YRI][hapmap]
rs6697620	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698495	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520022	0.86[YRI][hapmap]
rs878471	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs9733	0.86[YRI][hapmap]
rs9803935	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1053732	HORMAD1	cis	Nerve Tibial	GTEx
rs1053732	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs1053732	HORMAD1	cis	Esophagus Mucosa	GTEx
rs1053732	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs1053732	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs1053732	HORMAD1	cis	uninvolved skin	skin_eQTL
rs1053732	ARNT	cis	normal skin	skin_eQTL
rs1053732	ARNT	cis	Thyroid	GTEx
rs1053732	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs1053732	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs1053732	HORMAD1	cis	normal skin	skin_eQTL
rs1053732	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs1053732	CTSS	cis	Nerve Tibial	GTEx
rs1053732	GOLPH3L	cis	Nerve Tibial	GTEx
rs1053732	HORMAD1	cis	lesional skin	skin_eQTL
rs1053732	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs1053732	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150584400-150600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:150584800-150600200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150585000-150600000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:150585200-150600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:150586600-150600400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:150587800-150598800	Strong transcription	Dnd41	blood
7	chr1:150587800-150600000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:150587800-150600400	Strong transcription	Brain Germinal Matrix	brain
9	chr1:150588200-150600200	Strong transcription	Fetal Intestine Large	intestine
10	chr1:150588600-150601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:150591400-150599800	Strong transcription	Fetal Brain Female	brain
12	chr1:150591600-150599800	Strong transcription	Fetal Lung	lung
13	chr1:150591600-150600000	Strong transcription	Thymus	Thymus
14	chr1:150591800-150600600	Genic enhancers	HMEC	breast
15	chr1:150592000-150599600	Strong transcription	Fetal Kidney	kidney
16	chr1:150592200-150599000	Genic enhancers	K562	blood
17	chr1:150592600-150600400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150592800-150600200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:150592800-150600200	Strong transcription	Fetal Intestine Small	intestine
20	chr1:150593000-150599400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:150593000-150600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:150593000-150600600	Strong transcription	Fetal Stomach	stomach
23	chr1:150593200-150600000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:150593200-150600400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:150593400-150600400	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:150593600-150600200	Strong transcription	Osteobl	bone
27	chr1:150594200-150598200	Strong transcription	Brain Hippocampus Middle	brain
28	chr1:150594200-150599800	Strong transcription	HSMMtube	muscle
29	chr1:150594200-150600000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:150594200-150600000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:150594200-150600200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:150594200-150600200	Strong transcription	Colon Smooth Muscle	Colon
33	chr1:150594200-150600400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:150594200-150600600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:150594400-150598000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:150594400-150598600	Strong transcription	Aorta	Aorta
37	chr1:150594400-150599000	Strong transcription	Fetal Brain Male	brain
38	chr1:150594400-150599800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:150594400-150600000	Strong transcription	Colonic Mucosa	Colon
40	chr1:150594400-150600200	Strong transcription	NH-A	brain
41	chr1:150594600-150600000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:150594600-150600200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:150594600-150600200	Strong transcription	HSMM	muscle
44	chr1:150594800-150599600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:150594800-150599800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:150594800-150600000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:150594800-150600000	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:150594800-150600200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:150595000-150598400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:150595000-150600000	Strong transcription	H1 Cell Line	embryonic stem cell

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