Variant report

Variant	rs12142733
Chromosome Location	chr1:153860241-153860242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:153860089-153860436	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153858733..153861625-chr1:153893307..153895024,2	K562	blood:
2	chr1:153858652..153861331-chr1:153892093..153894371,2	MCF-7	breast:
3	chr1:153860125..153863028-chr1:153893524..153895754,2	K562	blood:
4	chr1:153857419..153860844-chr1:153877068..153879565,3	K562	blood:
5	chr1:153854622..153856492-chr1:153859608..153861522,2	K562	blood:
6	chr1:153850041..153853026-chr1:153858590..153860683,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236327	TF binding region
ENSG00000143614	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10127484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494303	0.88[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10908512	0.90[EUR][1000 genomes]
rs10908525	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11264573	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264736	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1127091	0.83[AFR][1000 genomes]
rs1139620	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11800001	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124424	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130611	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133492	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133923	0.85[AFR][1000 genomes]
rs12142639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738361	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.83[YRI][hapmap]
rs2790690	0.83[YRI][hapmap]
rs2841108	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.81[YRI][hapmap]
rs3001365	1.00[CHB][hapmap]
rs35711150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791186	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4276953	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4370789	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451582	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4540690	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4581307	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4596938	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4845360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap]
rs61803655	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6427300	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427306	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661009	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668066	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6677794	0.81[AFR][1000 genomes]
rs6690619	0.81[AFR][1000 genomes]
rs72694233	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7414227	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415004	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522030	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549032	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7554469	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426935	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9426938	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9427232	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9427233	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12142733	GBA	cis	parietal	SCAN
rs12142733	HAX1	cis	cerebellum	SCAN
rs12142733	S100A8	cis	parietal	SCAN
rs12142733	SLC27A3	cis	cerebellum	SCAN
rs12142733	PSMD4	cis	parietal	SCAN
rs12142733	THEM5	cis	parietal	SCAN
rs12142733	GATAD2B	cis	cerebellum	SCAN
rs12142733	DCST2	cis	cerebellum	SCAN
rs12142733	S100A13	cis	lymphoblastoid	seeQTL
rs12142733	CTAG2	trans	parietal	SCAN
rs12142733	GATAD2B	cis	parietal	SCAN
rs12142733	GATAD2B	cis	multi-tissue	Pritchard
rs12142733	FLG	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:153842800-153862800	Weak transcription	Thymus	Thymus
6	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
7	chr1:153846400-153871600	Weak transcription	Lung	lung
8	chr1:153853800-153864800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:153853800-153892200	Weak transcription	Pancreas	Pancrea
10	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:153854000-153869200	Weak transcription	HepG2	liver
12	chr1:153854000-153892600	Weak transcription	Colonic Mucosa	Colon
13	chr1:153854400-153876200	Weak transcription	Spleen	Spleen
14	chr1:153854400-153892400	Weak transcription	Aorta	Aorta
15	chr1:153854600-153865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:153854600-153892200	Weak transcription	HSMM	muscle
17	chr1:153854800-153871200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:153855000-153861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:153855000-153866200	Weak transcription	Left Ventricle	heart
20	chr1:153855000-153886800	Weak transcription	Gastric	stomach
21	chr1:153855000-153886800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:153855000-153887200	Weak transcription	Ovary	ovary
23	chr1:153855000-153891800	Weak transcription	NHEK	skin
24	chr1:153855000-153892400	Weak transcription	NHLF	lung
25	chr1:153855000-153892800	Weak transcription	NH-A	brain
26	chr1:153855200-153860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:153855200-153862400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:153855200-153865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:153855200-153865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:153855200-153871200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:153855200-153871200	Weak transcription	Fetal Brain Female	brain
32	chr1:153855200-153880600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:153855400-153860800	Weak transcription	Fetal Lung	lung
34	chr1:153855400-153861000	Weak transcription	NHDF-Ad	bronchial
35	chr1:153855400-153861200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:153855400-153865200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:153855400-153870400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:153855400-153871200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:153855400-153876400	Weak transcription	Osteobl	bone
40	chr1:153855400-153879600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:153855400-153892000	Weak transcription	HMEC	breast
42	chr1:153855600-153860800	Weak transcription	Liver	Liver
43	chr1:153855600-153860800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:153855600-153861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:153855600-153861200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:153855600-153863000	Weak transcription	Fetal Stomach	stomach
47	chr1:153855600-153865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:153855600-153865000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:153855600-153865400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:153855600-153869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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