Variant report

Variant	rs1590501
Chromosome Location	chr13:30456307-30456308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30437563..30440541-chr13:30455338..30457751,2	MCF-7	breast:
2	chr13:30423330..30425748-chr13:30454426..30456946,2	MCF-7	breast:
3	chr13:30455431..30458403-chr13:30460458..30462346,2	K562	blood:
4	chr13:30455592..30458193-chr13:30464245..30465781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236258	Chromatin interaction
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1033930	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11616444	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11618268	0.83[ASN][1000 genomes]
rs11620360	1.00[CHB][hapmap]
rs278040	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4512947	0.80[EUR][1000 genomes]
rs6490432	0.80[EUR][1000 genomes]
rs7994929	0.98[EUR][1000 genomes]
rs912396	1.00[CHB][hapmap]
rs9314986	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508573	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1590501	SHISA2	cis	cerebellum	SCAN
rs1590501	PAN3	cis	parietal	SCAN
rs1590501	EXOSC6	trans	cerebellum	SCAN
rs1590501	SLC7A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30449600-30458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:30450000-30457000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:30452200-30461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:30452200-30468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:30452200-30468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:30452600-30458200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:30452600-30458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:30452600-30472200	Weak transcription	Ovary	ovary
9	chr13:30452800-30458200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:30452800-30458200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:30452800-30458200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:30453200-30458600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:30454800-30456400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:30455000-30458200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:30455800-30456400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr13:30455800-30456400	Enhancers	Brain Hippocampus Middle	brain
17	chr13:30455800-30457200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:30455800-30457200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr13:30456000-30457400	Weak transcription	Fetal Intestine Small	intestine
20	chr13:30456000-30459200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:30456200-30456600	Enhancers	Brain Anterior Caudate	brain
22	chr13:30456200-30458200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:30456200-30462800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links