Variant report

Variant	rs1278493
Chromosome Location	chr3:135814009-135814010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135812577..135814878-chr3:135819697..135822271,2	K562	blood:
2	chr3:135812554..135814672-chr3:135913770..135915679,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10935177	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];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1153877	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs1154988	1.00[JPT][hapmap]
rs1279425	0.86[JPT][hapmap]
rs1279831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1279840	0.86[JPT][hapmap]
rs3755636	0.86[JPT][hapmap]
rs3957816	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4678428	0.86[JPT][hapmap]
rs548288	0.86[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs606725	0.86[JPT][hapmap]
rs642075	0.82[EUR][1000 genomes]
rs645040	1.00[JPT][hapmap]
rs661739	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs684773	1.00[JPT][hapmap]
rs687339	1.00[JPT][hapmap]
rs7349597	0.82[EUR][1000 genomes]
rs7372313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs895894	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9810089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs9840812	1.00[JPT][hapmap]
rs9845457	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1278493	NMT2	trans	lymphoblastoid	seeQTL
rs1278493	PPP2R3A	cis	cerebellum	SCAN
rs1278493	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs1278493	PCCB	cis	cerebellum	SCAN
rs1278493	PCCB	cis	parietal	SCAN
rs1278493	PCCB	cis	lymphoblastoid	seeQTL
rs1278493	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
2	chr3:135800400-135815400	Strong transcription	Stomach Smooth Muscle	stomach
3	chr3:135803000-135826600	Weak transcription	Liver	Liver
4	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:135803600-135821600	Weak transcription	Right Ventricle	heart
6	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
7	chr3:135803800-135832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:135803800-135860000	Weak transcription	NHLF	lung
9	chr3:135804000-135814800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:135804000-135832000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:135804000-135833200	Weak transcription	HMEC	breast
12	chr3:135804200-135819400	Weak transcription	Colonic Mucosa	Colon
13	chr3:135804600-135822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:135805200-135832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:135805200-135832800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:135805400-135843800	Weak transcription	NHEK	skin
17	chr3:135807200-135822000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:135807400-135833200	Weak transcription	Lung	lung
19	chr3:135808800-135814800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:135809200-135816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:135809400-135815000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:135809600-135814400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:135810000-135816200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:135810000-135828800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:135810200-135822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:135810200-135822200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:135810200-135825600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:135810200-135827800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:135810200-135832800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:135810200-135835600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:135810200-135835800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:135810400-135819600	Weak transcription	HSMMtube	muscle
33	chr3:135810400-135820800	Weak transcription	Fetal Kidney	kidney
34	chr3:135810400-135820800	Weak transcription	Left Ventricle	heart
35	chr3:135810400-135820800	Weak transcription	Ovary	ovary
36	chr3:135810400-135821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:135810400-135821400	Weak transcription	Fetal Brain Female	brain
38	chr3:135810400-135821600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:135810400-135822000	Weak transcription	Brain Germinal Matrix	brain
40	chr3:135810400-135822000	Weak transcription	Fetal Intestine Large	intestine
41	chr3:135810400-135822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:135810400-135822200	Weak transcription	Aorta	Aorta
43	chr3:135810400-135822200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:135810400-135824000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:135810400-135824200	Weak transcription	Pancreas	Pancrea
46	chr3:135810400-135827000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:135810400-135828800	Weak transcription	Brain Substantia Nigra	brain
48	chr3:135810400-135830800	Weak transcription	Fetal Brain Male	brain
49	chr3:135810400-135831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:135810400-135832000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links