Variant report

Variant	rs2408301
Chromosome Location	chr13:51808916-51808917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10492520	0.82[MEX][hapmap]
rs12584566	1.00[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs17837199	0.81[AMR][1000 genomes]
rs2148527	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9563039	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568554	0.90[AMR][1000 genomes]
rs9568557	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568558	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2408301	NDUFC2	trans	brain	seeQTL
rs2408301	HLA-G	trans	brain	seeQTL
rs2408301	CTU1	trans	brain	seeQTL
rs2408301	TREML1	trans	brain	seeQTL
rs2408301	PTGS2	trans	brain	seeQTL
rs2408301	CCL3	trans	brain	seeQTL
rs2408301	KRTAP10-10	trans	brain	seeQTL
rs2408301	EGFL6	trans	lymphoblastoid	seeQTL
rs2408301	RBM3	trans	brain	seeQTL
rs2408301	DUSP6	trans	brain	seeQTL
rs2408301	CH25H	trans	brain	seeQTL
rs2408301	METTL2B	trans	brain	seeQTL
rs2408301	LYRM7	trans	brain	seeQTL
rs2408301	FSIP2	trans	brain	seeQTL
rs2408301	METTL2A	trans	brain	seeQTL
rs2408301	APOLD1	trans	brain	seeQTL
rs2408301	DAPP1	trans	brain	seeQTL
rs2408301	SIK1	trans	brain	seeQTL
rs2408301	EGR2	trans	brain	seeQTL
rs2408301	KCNH6	trans	brain	seeQTL
rs2408301	RSAD2	trans	brain	seeQTL
rs2408301	ADAMTS1	trans	brain	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51799600-51809000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:51799600-51809800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:51799800-51818200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:51803600-51809800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:51805000-51809000	Weak transcription	Right Ventricle	heart
6	chr13:51805000-51809800	Weak transcription	Lung	lung
7	chr13:51805200-51809000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:51805200-51809000	Weak transcription	HUVEC	blood vessel
9	chr13:51805200-51809400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:51805200-51809600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:51805200-51809800	Weak transcription	Left Ventricle	heart
12	chr13:51805200-51809800	Weak transcription	Right Atrium	heart
13	chr13:51805200-51825600	Weak transcription	Aorta	Aorta
14	chr13:51805400-51809800	Weak transcription	Adipose Nuclei	Adipose
15	chr13:51805400-51810600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:51805800-51809600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:51805800-51809800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:51806000-51809800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:51806000-51810000	Weak transcription	Fetal Brain Male	brain
20	chr13:51806200-51814000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr13:51807000-51809400	Weak transcription	Brain Germinal Matrix	brain
22	chr13:51807200-51810000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr13:51807400-51809800	Weak transcription	Colon Smooth Muscle	Colon
24	chr13:51807400-51810200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
25	chr13:51807600-51810000	Weak transcription	Spleen	Spleen
26	chr13:51808000-51809000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:51808000-51810200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:51808000-51810200	Enhancers	Brain Hippocampus Middle	brain
29	chr13:51808000-51810200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:51808000-51810400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:51808000-51810600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
32	chr13:51808000-51812600	Enhancers	Brain Cingulate Gyrus	brain
33	chr13:51808000-51821200	Enhancers	Brain Substantia Nigra	brain
34	chr13:51808200-51809000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr13:51808200-51810400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr13:51808200-51810600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:51808400-51809200	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr13:51808400-51810000	Strong transcription	Fetal Stomach	stomach
39	chr13:51808400-51810200	Enhancers	Fetal Kidney	kidney
40	chr13:51808400-51814400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:51808400-51821400	Enhancers	Fetal Heart	heart
42	chr13:51808600-51809000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr13:51808600-51809800	Weak transcription	Brain Anterior Caudate	brain
44	chr13:51808600-51810000	Weak transcription	Brain Angular Gyrus	brain
45	chr13:51808600-51820000	Weak transcription	Fetal Brain Female	brain
46	chr13:51808800-51809000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr13:51808800-51814000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:51808800-51816400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links