Variant report

Variant	rs2788168
Chromosome Location	chr1:209373577-209373578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209368320..209369917-chr1:209372141..209373660,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11586407	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11586451	0.84[ASN][1000 genomes]
rs12722814	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755287	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1933612	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1933619	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2266024	0.84[EUR][1000 genomes]
rs2489651	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788158	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788159	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788161	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788162	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788170	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970555	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970556	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970560	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996683	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996687	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2996688	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523921	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944110	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396124	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4402132	0.84[ASN][1000 genomes]
rs6658956	0.82[ASN][1000 genomes]
rs6672407	0.84[ASN][1000 genomes]
rs66763810	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678963	0.82[ASN][1000 genomes]
rs6692414	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6704132	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71636106	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209371600-209373800	Enhancers	H1 Cell Line	embryonic stem cell
3	chr1:209371800-209373600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:209372000-209373600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:209372000-209374200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr1:209372200-209373800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:209372400-209373600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:209372400-209373800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:209372400-209373800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:209372800-209373600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:209372800-209373600	Enhancers	Brain Germinal Matrix	brain
12	chr1:209372800-209373600	Enhancers	Fetal Brain Male	brain
13	chr1:209373200-209373800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:209373200-209373800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:209373200-209374000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:209373200-209374200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:209373400-209373600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:209373400-209373600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:209373400-209373600	Enhancers	Fetal Intestine Large	intestine
22	chr1:209373400-209373800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:209373400-209376200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links