Variant report

Variant	rs11204679
Chromosome Location	chr1:150583670-150583671
allele	C/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150550613..150553020-chr1:150582726..150586821,4	MCF-7	breast:
2	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
3	chr1:150581828..150584302-chr1:150897421..150900284,2	MCF-7	breast:
4	chr1:150575837..150580445-chr1:150580466..150584080,8	K562	blood:
5	chr1:150575837..150579446-chr1:150579554..150584365,8	K562	blood:
6	chr1:150579544..150581057-chr1:150582550..150584092,2	K562	blood:
7	chr1:150544073..150554289-chr1:150582699..150598712,61	K562	blood:

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888384	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888385	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204668	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204669	0.87[ASN][1000 genomes]
rs11204675	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204677	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204678	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204684	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11585169	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116492	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12125672	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126271	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12139563	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406712	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12746899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971378	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048558	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738484	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738485	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754209	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970918	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970923	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971041	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55862611	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61820165	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669122	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697620	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698495	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878471	0.92[ASN][1000 genomes]
rs932054	0.85[ASN][1000 genomes]
rs9803935	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11204679	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204679	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204679	HORMAD1	cis	Nerve Tibial	GTEx
rs11204679	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204679	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204679	CTSS	cis	Nerve Tibial	GTEx
rs11204679	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204679	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204679	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204679	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204679	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204679	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204679	ARNT	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
2	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
3	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:150566400-150583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:150571000-150583800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:150573400-150584200	Weak transcription	Thymus	Thymus
7	chr1:150573400-150587800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:150573600-150583800	Weak transcription	Fetal Brain Female	brain
9	chr1:150573600-150583800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:150576200-150591000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:150577000-150588400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:150577400-150585800	Weak transcription	Aorta	Aorta
13	chr1:150577400-150587800	Weak transcription	Esophagus	oesophagus
14	chr1:150577600-150584000	Weak transcription	Right Ventricle	heart
15	chr1:150577600-150584600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:150577800-150583800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:150578000-150592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150579400-150583800	Weak transcription	K562	blood
19	chr1:150581600-150584800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:150581600-150585800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:150581600-150587000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:150581800-150584600	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:150581800-150584800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:150581800-150585600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:150581800-150585600	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:150581800-150586000	Enhancers	Brain Hippocampus Middle	brain
27	chr1:150582000-150583800	Enhancers	NHEK	skin
28	chr1:150582000-150585400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:150582000-150585800	Enhancers	Adipose Nuclei	Adipose
30	chr1:150582200-150583800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:150582200-150584200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr1:150582200-150584200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:150582200-150584400	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:150582200-150584600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:150582200-150584600	Enhancers	Brain Anterior Caudate	brain
36	chr1:150582200-150584800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:150582200-150586800	Enhancers	Left Ventricle	heart
38	chr1:150582200-150587800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:150582200-150588800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:150582400-150583800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:150582400-150583800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:150582400-150583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:150582400-150583800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:150582400-150584000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:150582400-150585800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:150582400-150588800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:150582400-150594400	Weak transcription	Ovary	ovary
48	chr1:150582600-150583800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:150582600-150583800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:150582600-150583800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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