Variant report

Variant	rs61822631
Chromosome Location	chr1:223858255-223858256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223858240-223858390	HBMEC	blood vessel:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
2	CTCF	chr1:223858241-223858459	MCF-7	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
3	RAD21	chr1:223858139-223858544	SK-N-SH_RA	brain:	n/a	chr1:223858354-223858373
4	CTCF	chr1:223858240-223858390	HVMF	connective:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
5	RAD21	chr1:223858110-223858691	MCF-7	breast:	n/a	chr1:223858354-223858373
6	RAD21	chr1:223858165-223858545	HepG2	liver:	n/a	chr1:223858354-223858373
7	CTCF	chr1:223858180-223858330	WI-38	lung:	n/a	n/a
8	CTCF	chr1:223858020-223858601	MCF-7	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
9	RAD21	chr1:223858041-223858556	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
10	CTCF	chr1:223858240-223858390	GM12870	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
11	RAD21	chr1:223858130-223858623	HepG2	liver:	n/a	chr1:223858354-223858373
12	CTCF	chr1:223858233-223858459	Fibrobl	skin:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
13	MYC	chr1:223858177-223858485	MCF10A-Er-Src	breast:	n/a	n/a
14	RAD21	chr1:223858190-223858410	K562	blood:	n/a	chr1:223858354-223858373
15	RAD21	chr1:223858085-223858725	MCF-7	breast:	n/a	chr1:223858354-223858373
16	CTCF	chr1:223858238-223858486	Pancreas_OC	pancreas:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
17	CTCF	chr1:223858221-223858498	Gliobla	brain:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
18	CTCF	chr1:223858234-223858459	H1-hESC	embryonic stem cell:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
19	CTCF	chr1:223858168-223858662	MCF-7	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
20	CTCF	chr1:223858240-223858390	HAc	cerebellar:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
21	RAD21	chr1:223858204-223858447	GM12878	blood:	n/a	chr1:223858354-223858373
22	CTCF	chr1:223858192-223858456	A549	lung:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
23	JUND	chr1:223858193-223858476	K562	blood:	n/a	n/a
24	CTCF	chr1:223858231-223858456	GM12891	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
25	JUND	chr1:223858180-223858778	H1-hESC	embryonic stem cell:	n/a	chr1:223858667-223858679 chr1:223858669-223858678 chr1:223858669-223858676 chr1:223858668-223858678 chr1:223858668-223858678
26	RAD21	chr1:223858190-223858425	GM12878	blood:	n/a	chr1:223858354-223858373
27	RFX5	chr1:223858251-223858382	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr1:223858115-223858560	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
29	CTCF	chr1:223857989-223858671	HCT-116	colon:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
30	CTCF	chr1:223858240-223858390	BE2_C	brain:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
31	CTCF	chr1:223858142-223858529	T-47D	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
32	CTCF	chr1:223858120-223858496	HepG2	liver:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
33	ZNF263	chr1:223858155-223858551	HEK293-T-REx	kidney:	n/a	n/a
34	CTCF	chr1:223858240-223858390	GM12869	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
35	CTCF	chr1:223858249-223858470	Lung_OC	lung:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
36	SMC3	chr1:223858090-223858508	GM12878	blood:	n/a	chr1:223858358-223858372
37	CTCF	chr1:223858068-223858656	K562	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
38	CTCF	chr1:223858175-223858553	GM12878	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
39	RAD21	chr1:223858016-223858634	HCT-116	colon:	n/a	chr1:223858354-223858373
40	MAFK	chr1:223858166-223858507	K562	blood:	n/a	n/a
41	CTCF	chr1:223858233-223858465	GM12892	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
42	RAD21	chr1:223858099-223858553	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
43	CTCF	chr1:223858221-223858472	GM19238	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
44	HCFC1	chr1:223858173-223858518	K562	blood:	n/a	n/a
45	CTCF	chr1:223858241-223858457	MCF-7	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
46	CTCF	chr1:223858163-223858551	K562	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
47	CTCF	chr1:223858231-223858502	GM12878	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
48	CTCF	chr1:223858230-223858522	K562	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
49	RAD21	chr1:223858147-223858543	IMR90	lung:	n/a	chr1:223858354-223858373
50	CTCF	chr1:223858249-223858479	LNCaP	prostate:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371

No.	Distal block	Cell Line	Cell type
1	chr1:223305268..223307186-chr1:223856777..223859694,2	K562	blood:
2	chr1:223840739..223843292-chr1:223856581..223858792,2	MCF-7	breast:
3	chr1:223819090..223819750-chr1:223857938..223858740,2	MCF-7	breast:
4	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:
5	chr1:223815914..223816546-chr1:223857853..223858702,2	K562	blood:
6	chr1:223857293..223858818-chr1:223866737..223869584,2	K562	blood:
7	chr1:223838928..223839586-chr1:223857876..223858715,2	MCF-7	breast:
8	chr1:223852049..223854014-chr1:223857086..223858680,2	MCF-7	breast:

Variant related genes	Relation type
CAPN8	TF binding region
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10799550	0.87[EUR][1000 genomes]
rs12567519	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568612	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17556570	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1936525	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41307690	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4511081	0.89[EUR][1000 genomes]
rs4653522	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59990581	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61450747	0.87[EUR][1000 genomes]
rs61822582	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61822583	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61822586	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61822630	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61822632	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822633	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822634	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822635	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822636	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823962	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823965	0.89[EUR][1000 genomes]
rs61825227	0.88[EUR][1000 genomes]
rs6656416	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690568	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702314	0.90[EUR][1000 genomes]
rs6702430	0.89[EUR][1000 genomes]
rs7551783	1.00[AMR][1000 genomes];1.00[EUR][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	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	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
3	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
4	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61822631	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:223855400-223859600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:223855800-223865800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223856800-223862200	Weak transcription	Pancreas	Pancrea
5	chr1:223857000-223858800	Weak transcription	Colonic Mucosa	Colon
6	chr1:223857400-223859400	Enhancers	NHDF-Ad	bronchial
7	chr1:223858000-223858600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:223858200-223858600	Enhancers	Stomach Mucosa	stomach
9	chr1:223858200-223858800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:223858200-223859000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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