Variant report

Variant	rs1340546
Chromosome Location	chr13:51723601-51723602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51722837..51724133-chr13:51860193..51861210,11	MCF-7	breast:
2	chr13:51722919..51723811-chr13:51860090..51861195,8	MCF-7	breast:
3	chr13:51722852..51723780-chr13:51858091..51858924,2	MCF-7	breast:

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs35362741	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv900079	chr13:51711436-51739168	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv900080	chr13:51711436-51754873	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1340546	LOC220429	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51719800-51725200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:51720400-51724000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr13:51720600-51724000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:51720600-51724400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:51720600-51724600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr13:51720600-51725200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr13:51720600-51731600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:51720800-51724600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:51721600-51728600	Weak transcription	Spleen	Spleen
10	chr13:51722000-51724000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:51722200-51724000	Enhancers	Brain Anterior Caudate	brain
12	chr13:51722400-51723800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr13:51722800-51723800	Enhancers	Fetal Lung	lung
14	chr13:51722800-51724000	Enhancers	Brain Cingulate Gyrus	brain
15	chr13:51723000-51723800	Enhancers	Brain Angular Gyrus	brain
16	chr13:51723000-51724000	Enhancers	Brain Hippocampus Middle	brain
17	chr13:51723000-51724200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr13:51723000-51727000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:51723200-51725200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr13:51723200-51725200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr13:51723200-51725400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr13:51723200-51725400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr13:51723200-51725800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr13:51723200-51726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr13:51723200-51727000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr13:51723200-51727800	Weak transcription	HUVEC	blood vessel
27	chr13:51723200-51732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:51723400-51723800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:51723400-51724000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:51723400-51724000	Enhancers	Fetal Brain Male	brain
31	chr13:51723600-51723800	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links