Variant report

Variant	rs592724
Chromosome Location	chr13:30624499-30624500
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	chr13:30623546..30625810-chr13:30634555..30637096,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1041578	0.99[ASN][1000 genomes]
rs1041579	1.00[ASN][1000 genomes]
rs60575810	1.00[ASN][1000 genomes]
rs61003849	1.00[ASN][1000 genomes]
rs626014	0.99[ASN][1000 genomes]
rs66566952	1.00[ASN][1000 genomes]
rs67365184	1.00[ASN][1000 genomes]
rs9551805	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs592724	FAM123A	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30612000-30625600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:30614800-30625800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:30619400-30625600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr13:30620200-30626600	Weak transcription	Stomach Mucosa	stomach
5	chr13:30620800-30625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:30622000-30625800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:30622200-30625800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:30622200-30625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr13:30622200-30626000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr13:30622400-30625600	Weak transcription	Primary T cells from cord blood	blood
11	chr13:30622400-30625600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:30622400-30625800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr13:30622400-30625800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:30622400-30625800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:30622400-30625800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:30622400-30626200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:30622400-30626200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr13:30622600-30625600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr13:30622800-30625800	Weak transcription	Fetal Intestine Small	intestine
20	chr13:30623600-30624800	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links