Variant report

Variant	rs6669428
Chromosome Location	chr1:210525509-210525510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210522606..210528458-chr1:210543936..210548857,12	MCF-7	breast:
2	chr1:210316799..210319752-chr1:210525162..210527241,2	MCF-7	breast:
3	chr1:210524143..210528832-chr1:210543639..210547917,8	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10489388	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12729428	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17016026	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17759021	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890303	0.82[CHD][hapmap]
rs2357583	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765872	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765879	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765884	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs60935759	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828656	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540589	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656628	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6677509	0.84[CEU][hapmap]
rs6690120	0.83[CEU][hapmap]
rs7354957	0.83[EUR][1000 genomes]
rs7355019	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs742560	0.84[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs7527939	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7530104	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7550408	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550554	0.84[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs761171	0.88[CEU][hapmap];0.82[EUR][1000 genomes]

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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6669428	ELK4	cis	cerebellum	SCAN
rs6669428	PLXNA2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210516800-210534400	Weak transcription	Fetal Lung	lung
4	chr1:210517000-210531400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:210517000-210534400	Weak transcription	HSMM	muscle
6	chr1:210517200-210534400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:210517200-210534400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:210517200-210534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:210517200-210535800	Weak transcription	Right Ventricle	heart
10	chr1:210517200-210536000	Weak transcription	Fetal Stomach	stomach
11	chr1:210517200-210536000	Weak transcription	Left Ventricle	heart
12	chr1:210517400-210533200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:210517400-210534400	Weak transcription	Adipose Nuclei	Adipose
14	chr1:210517600-210536000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:210518600-210534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:210520800-210531800	Weak transcription	HSMMtube	muscle
17	chr1:210521000-210532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:210521000-210534400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:210521200-210534400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:210521400-210534400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:210522200-210525600	Weak transcription	Fetal Heart	heart
22	chr1:210522200-210526200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:210522600-210537600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:210523000-210534400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:210525000-210526600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:210525200-210538000	Weak transcription	Ovary	ovary
27	chr1:210525400-210526000	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links