Variant report

Variant	rs7336182
Chromosome Location	chr13:52413152-52413153
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	chr13:52390628..52392795-chr13:52410720..52413468,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12874582	1.00[ASN][1000 genomes]
rs12876049	0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs17076052	1.00[ASN][1000 genomes]
rs1924614	1.00[ASN][1000 genomes]
rs1924615	1.00[ASN][1000 genomes]
rs1924618	1.00[ASN][1000 genomes]
rs2408530	1.00[ASN][1000 genomes]
rs28429889	1.00[ASN][1000 genomes]
rs28485335	1.00[ASN][1000 genomes]
rs34507703	1.00[ASN][1000 genomes]
rs34595679	1.00[ASN][1000 genomes]
rs35382547	1.00[ASN][1000 genomes]
rs35824984	1.00[ASN][1000 genomes]
rs4605048	1.00[ASN][1000 genomes]
rs549831	1.00[ASN][1000 genomes]
rs575555	1.00[ASN][1000 genomes]
rs577331	1.00[ASN][1000 genomes]
rs578134	1.00[ASN][1000 genomes]
rs579839	1.00[ASN][1000 genomes]
rs58050745	1.00[ASN][1000 genomes]
rs58919798	1.00[ASN][1000 genomes]
rs61957362	1.00[ASN][1000 genomes]
rs61957363	1.00[ASN][1000 genomes]
rs61957365	1.00[ASN][1000 genomes]
rs61957367	1.00[ASN][1000 genomes]
rs61957391	1.00[ASN][1000 genomes]
rs61957414	1.00[ASN][1000 genomes]
rs7323551	1.00[ASN][1000 genomes]
rs7333241	1.00[ASN][1000 genomes]
rs7338168	1.00[ASN][1000 genomes]
rs932912	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv900081	chr13:52406404-52426096	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7336182	NEK3	cis	parietal	SCAN
rs7336182	LOC440138	cis	multi-tissue	Pritchard
rs7336182	CAB39L	cis	parietal	SCAN
rs7336182	VPS36	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52393600-52418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:52401600-52419200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr13:52404800-52413800	Weak transcription	Fetal Intestine Small	intestine
4	chr13:52406600-52414200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr13:52409200-52419200	Weak transcription	Right Atrium	heart
6	chr13:52410400-52415400	Weak transcription	Brain Anterior Caudate	brain
7	chr13:52410800-52413400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr13:52411400-52413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:52411800-52413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:52411800-52413600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:52412000-52413200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:52412200-52413200	Enhancers	NHDF-Ad	bronchial
13	chr13:52412400-52413200	Enhancers	HSMMtube	muscle
14	chr13:52412400-52413600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:52412600-52413200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:52412800-52413800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:52413000-52415200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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