Variant report

Variant	rs12045807
Chromosome Location	chr1:150584834-150584835
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr1:150583951..150586668-chr1:150586711..150588335,2	K562	blood:
4	chr1:150550493..150552164-chr1:150583866..150586279,2	MCF-7	breast:
5	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
6	chr1:150584201..150586681-chr1:150587631..150590116,2	MCF-7	breast:
7	chr1:150575574..150579805-chr1:150584520..150587966,8	K562	blood:
8	chr1:150575672..150578383-chr1:150583826..150586849,3	MCF-7	breast:
9	chr1:150532483..150534415-chr1:150583903..150587502,3	K562	blood:
10	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-GOLPH3L-1	chr1:150583859-150585487	ENSG00000246674

No data

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

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1053701	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204665	0.84[CEU][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs11204674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204689	0.90[EUR][1000 genomes]
rs11204700	0.83[EUR][1000 genomes]
rs11204727	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11576175	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11585460	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12031458	0.90[EUR][1000 genomes]
rs12032445	0.90[EUR][1000 genomes]
rs12034302	0.92[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12036914	0.82[ASN][1000 genomes]
rs12038403	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12042580	0.82[ASN][1000 genomes]
rs16840074	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3754207	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4379678	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs4970970	0.90[EUR][1000 genomes]
rs55890313	0.90[EUR][1000 genomes]
rs60060012	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817598	0.80[EUR][1000 genomes]
rs61820166	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61820168	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61820170	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587515	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587517	0.90[EUR][1000 genomes]
rs6672667	0.82[ASN][1000 genomes]
rs7517	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520511	0.82[EUR][1000 genomes]
rs7520516	0.82[EUR][1000 genomes]
rs7543465	0.84[CEU][hapmap];0.92[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12045807	CTSK	cis	Artery Aorta	GTEx
rs12045807	LASS2	cis	Liver	GTEx

Chromatin state (count:126 , 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	chr1:150573400-150587800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:150576200-150591000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:150577000-150588400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150577400-150585800	Weak transcription	Aorta	Aorta
6	chr1:150577400-150587800	Weak transcription	Esophagus	oesophagus
7	chr1:150578000-150592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:150581600-150585800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:150581600-150587000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:150581800-150585600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:150581800-150585600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr1:150581800-150586000	Enhancers	Brain Hippocampus Middle	brain
13	chr1:150582000-150585400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:150582000-150585800	Enhancers	Adipose Nuclei	Adipose
15	chr1:150582200-150586800	Enhancers	Left Ventricle	heart
16	chr1:150582200-150587800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:150582200-150588800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:150582400-150585800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:150582400-150588800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:150582400-150594400	Weak transcription	Ovary	ovary
21	chr1:150582600-150591800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:150582800-150587800	Weak transcription	Fetal Brain Male	brain
23	chr1:150583000-150585800	Genic enhancers	HMEC	breast
24	chr1:150583000-150586400	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr1:150583000-150587000	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:150583000-150587600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:150583000-150588000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:150583200-150585800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:150583200-150585800	Enhancers	NH-A	brain
30	chr1:150583200-150585800	Enhancers	NHLF	lung
31	chr1:150583200-150586000	Genic enhancers	Fetal Thymus	thymus
32	chr1:150583200-150586800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:150583200-150586800	Enhancers	Pancreas	Pancrea
34	chr1:150583200-150588000	Genic enhancers	Fetal Intestine Small	intestine
35	chr1:150583200-150589000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:150583400-150585000	Enhancers	Stomach Mucosa	stomach
37	chr1:150583400-150585800	Enhancers	HUVEC	blood vessel
38	chr1:150583400-150588200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:150583600-150585400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
40	chr1:150583600-150585800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:150583600-150586400	Enhancers	Colonic Mucosa	Colon
42	chr1:150583600-150586400	Strong transcription	Dnd41	blood
43	chr1:150583600-150588000	Enhancers	Liver	Liver
44	chr1:150583800-150585200	Enhancers	Brain Substantia Nigra	brain
45	chr1:150583800-150585400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:150583800-150585600	Enhancers	Psoas Muscle	Psoas
47	chr1:150583800-150585800	Genic enhancers	K562	blood
48	chr1:150583800-150585800	Enhancers	NHDF-Ad	bronchial
49	chr1:150583800-150586200	Genic enhancers	Placenta	Placenta
50	chr1:150583800-150586600	Enhancers	Brain Angular Gyrus	brain

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