Variant report

Variant	rs9429817
Chromosome Location	chr1:209738214-209738215
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	chr1:209726680..209728557-chr1:209737495..209739643,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11119312	0.81[ASN][1000 genomes]
rs11576233	0.81[ASN][1000 genomes]
rs11587591	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs11589826	0.89[EUR][1000 genomes]
rs12144092	0.81[ASN][1000 genomes]
rs35913818	0.81[ASN][1000 genomes]
rs6690557	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs713075	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs7528698	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs7532726	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs7541562	0.81[ASN][1000 genomes]
rs9429816	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9429818	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs9429998	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9429999	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9429817	RP1-272L16.1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209726800-209738400	Weak transcription	NHEK	skin
2	chr1:209734400-209740600	Weak transcription	HSMM	muscle
3	chr1:209735800-209739000	Weak transcription	Fetal Brain Male	brain
4	chr1:209736400-209738400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:209737400-209738800	Enhancers	Fetal Stomach	stomach
6	chr1:209737800-209738400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr1:209737800-209739200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:209738000-209738800	Enhancers	Fetal Lung	lung
9	chr1:209738000-209739600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr1:209738000-209740000	Enhancers	Fetal Intestine Large	intestine
11	chr1:209738200-209738400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:209738200-209738400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:209738200-209738400	Enhancers	Esophagus	oesophagus
14	chr1:209738200-209738400	Enhancers	Fetal Kidney	kidney
15	chr1:209738200-209738400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
16	chr1:209738200-209738600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:209738200-209738600	Enhancers	Lung	lung
18	chr1:209738200-209738800	Enhancers	Fetal Intestine Small	intestine
19	chr1:209738200-209739000	Enhancers	Spleen	Spleen
20	chr1:209738200-209739200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:209738200-209739400	Enhancers	Fetal Brain Female	brain
22	chr1:209738200-209740600	Enhancers	HMEC	breast
23	chr1:209738200-209742000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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