Variant report

Variant	rs61825227
Chromosome Location	chr1:223829906-223829907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223827325..223830055-chr1:223836590..223838294,2	MCF-7	breast:
2	chr1:223823766..223826400-chr1:223828935..223830773,2	K562	blood:
3	chr1:223815744..223818238-chr1:223828274..223830462,2	K562	blood:

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12567519	0.84[EUR][1000 genomes]
rs12568612	0.84[EUR][1000 genomes]
rs17556570	0.84[EUR][1000 genomes]
rs1936525	0.86[EUR][1000 genomes]
rs41307690	0.88[EUR][1000 genomes]
rs4653522	0.88[EUR][1000 genomes]
rs61450747	0.99[EUR][1000 genomes]
rs61822582	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61822583	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61822586	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61822630	0.87[EUR][1000 genomes]
rs61822631	0.88[EUR][1000 genomes]
rs61822632	0.86[EUR][1000 genomes]
rs61822633	0.86[EUR][1000 genomes]
rs61822634	0.86[EUR][1000 genomes]
rs61822635	0.86[EUR][1000 genomes]
rs61822636	0.84[EUR][1000 genomes]
rs61823962	0.81[EUR][1000 genomes]
rs6656416	0.88[EUR][1000 genomes]
rs6690568	0.85[EUR][1000 genomes]
rs7551783	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61825227	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223822200-223833400	Weak transcription	Pancreas	Pancrea
2	chr1:223826400-223830400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr1:223826400-223831000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:223826400-223831200	Enhancers	Liver	Liver
5	chr1:223827200-223831000	Enhancers	Stomach Mucosa	stomach
6	chr1:223828000-223830400	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr1:223828200-223833400	Weak transcription	Colonic Mucosa	Colon
8	chr1:223828400-223830400	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:223828800-223834000	Weak transcription	Fetal Stomach	stomach
10	chr1:223829200-223830000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:223829200-223830200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:223829200-223830800	Enhancers	Fetal Intestine Small	intestine
13	chr1:223829400-223830800	Weak transcription	Gastric	stomach
14	chr1:223829400-223834000	Weak transcription	Lung	lung
15	chr1:223829600-223830200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:223829600-223831000	Enhancers	Fetal Intestine Large	intestine
17	chr1:223829800-223830400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:223829800-223830400	Enhancers	Fetal Lung	lung
19	chr1:223829800-223834400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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