Variant report

Variant	rs11617841
Chromosome Location	chr13:53536175-53536176
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	chr13:53225241..53227656-chr13:53534118..53536424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11618509	0.81[EUR][1000 genomes]
rs11618738	0.81[EUR][1000 genomes]
rs12867633	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12876856	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323112	0.81[EUR][1000 genomes]
rs1555559	0.81[EUR][1000 genomes]
rs1578872	0.81[EUR][1000 genomes]
rs34858262	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953476	1.00[ASN][1000 genomes]
rs35082723	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68164717	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7319859	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320575	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321464	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321816	0.91[EUR][1000 genomes]
rs7326351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327967	0.81[EUR][1000 genomes]
rs7996239	0.80[EUR][1000 genomes]
rs9316600	0.81[EUR][1000 genomes]
rs9316602	0.81[EUR][1000 genomes]
rs9536321	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536322	0.97[EUR][1000 genomes]
rs9536327	0.82[EUR][1000 genomes]
rs9568783	0.81[EUR][1000 genomes]
rs9568784	0.81[EUR][1000 genomes]
rs9568785	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9591484	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596733	0.83[EUR][1000 genomes]
rs986338	0.81[EUR][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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11617841	CCDC70	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53532800-53541000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:53533800-53540800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:53534400-53536200	Enhancers	Dnd41	blood
4	chr13:53534400-53536600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:53534600-53536200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:53534600-53538000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr13:53534800-53539000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:53535000-53536200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:53535000-53536400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr13:53535000-53536600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:53535000-53536600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr13:53535000-53538600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr13:53535200-53536400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr13:53535200-53536600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:53535400-53536200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr13:53535600-53536200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr13:53535600-53536800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:53535800-53536200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr13:53535800-53536400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:53535800-53536400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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