Variant report

Variant	rs6433000
Chromosome Location	chr2:168346441-168346442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1112983	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899757	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12105560	0.93[EUR][1000 genomes]
rs1227120	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1238298	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12466695	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996381	0.90[EUR][1000 genomes]
rs13032189	0.87[EUR][1000 genomes]
rs1431908	0.86[ASN][1000 genomes]
rs1541889	0.85[EUR][1000 genomes]
rs1653420	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653425	0.90[EUR][1000 genomes]
rs1653430	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16853648	0.86[EUR][1000 genomes]
rs1730713	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730725	0.86[EUR][1000 genomes]
rs1813255	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1919854	0.90[EUR][1000 genomes]
rs1919855	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983514	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523753	0.88[EUR][1000 genomes]
rs35580310	0.93[EUR][1000 genomes]
rs35827395	0.92[EUR][1000 genomes]
rs4667955	0.85[EUR][1000 genomes]
rs6710395	0.91[EUR][1000 genomes]
rs7567362	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491872	chr2:168220323-168737986	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3388045	chr2:168289403-168424317	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv834449	chr2:168340043-168511856	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6433000	SP5	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:168337000-168355400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:168337200-168348200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:168338200-168348200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:168338200-168366000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:168338400-168349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:168338400-168352400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:168341600-168352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:168341600-168352800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:168341600-168365200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:168342200-168352400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:168343600-168347600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:168343600-168352400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:168345600-168346800	Enhancers	Fetal Brain Male	brain
14	chr2:168345600-168347000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:168345600-168347200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr2:168345600-168347400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:168345800-168347200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:168345800-168347400	Enhancers	Colon Smooth Muscle	Colon
19	chr2:168346000-168346600	Enhancers	Brain Hippocampus Middle	brain
20	chr2:168346000-168347200	Enhancers	Fetal Muscle Leg	muscle
21	chr2:168346200-168346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:168346200-168347000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:168346200-168358800	Weak transcription	Fetal Lung	lung
24	chr2:168346400-168347200	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links