Variant report

Variant	rs4653522
Chromosome Location	chr1:223858133-223858134
allele	A/G
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	RAD21	chr1:223858110-223858691	MCF-7	breast:	n/a	chr1:223858354-223858373
2	CTCF	chr1:223858020-223858601	MCF-7	breast:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
3	RAD21	chr1:223858041-223858556	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
4	RAD21	chr1:223858130-223858623	HepG2	liver:	n/a	chr1:223858354-223858373
5	RAD21	chr1:223858085-223858725	MCF-7	breast:	n/a	chr1:223858354-223858373
6	RAD21	chr1:223858115-223858560	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
7	CTCF	chr1:223857989-223858671	HCT-116	colon:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
8	CTCF	chr1:223858120-223858496	HepG2	liver:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
9	SMC3	chr1:223858090-223858508	GM12878	blood:	n/a	chr1:223858358-223858372
10	CTCF	chr1:223858068-223858656	K562	blood:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
11	RAD21	chr1:223858016-223858634	HCT-116	colon:	n/a	chr1:223858354-223858373
12	RAD21	chr1:223858099-223858553	H1-hESC	embryonic stem cell:	n/a	chr1:223858354-223858373
13	CTCF	chr1:223858117-223858548	H1-hESC	embryonic stem cell:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
14	CTCF	chr1:223857954-223858748	A549	lung:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
15	CTCF	chr1:223858001-223858573	SK-N-SH	brain:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
16	RAD21	chr1:223857967-223858746	HCT-116	colon:	n/a	chr1:223858354-223858373
17	CTCF	chr1:223858051-223858633	HCT-116	colon:	n/a	chr1:223858357-223858373 chr1:223858351-223858372 chr1:223858356-223858374 chr1:223858358-223858371
18	RAD21	chr1:223858086-223858578	ECC-1	luminal epithelium:	n/a	chr1:223858354-223858373
19	RAD21	chr1:223858013-223858655	SK-N-SH	brain:	n/a	chr1:223858354-223858373
20	RAD21	chr1:223858003-223858648	A549	lung:	n/a	chr1:223858354-223858373
21	RAD21	chr1:223858102-223858607	ECC-1	luminal epithelium:	n/a	chr1:223858354-223858373
22	RAD21	chr1:223858117-223858508	HepG2	liver:	n/a	chr1:223858354-223858373

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: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10465524	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs10495215	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs10495216	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10495217	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10503144	0.85[CEU][hapmap]
rs10799550	0.87[EUR][1000 genomes]
rs10916634	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs10916646	0.87[CEU][hapmap]
rs12059770	0.85[CEU][hapmap]
rs12070364	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs12080250	0.85[CEU][hapmap]
rs12088254	0.85[CEU][hapmap]
rs12563637	0.85[CEU][hapmap]
rs12565967	0.85[CEU][hapmap]
rs12566817	0.85[CEU][hapmap]
rs12567519	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1419305	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs1629836	0.82[CEU][hapmap]
rs16842162	0.85[CEU][hapmap]
rs16842257	0.85[CEU][hapmap]
rs16842326	0.85[CEU][hapmap]
rs17556570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17557288	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557525	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17557623	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1779658	0.87[CEU][hapmap]
rs1892077	0.87[CEU][hapmap]
rs1936525	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186006	0.87[CEU][hapmap];0.96[TSI][hapmap]
rs41307690	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4511081	0.89[EUR][1000 genomes]
rs59990581	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61450747	0.87[EUR][1000 genomes]
rs61822582	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61822583	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61822586	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61822630	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61822631	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822632	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822633	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822634	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822635	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822636	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823962	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823965	0.89[EUR][1000 genomes]
rs61825227	0.88[EUR][1000 genomes]
rs6604724	0.85[CEU][hapmap]
rs6656416	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669046	0.87[CEU][hapmap]
rs6671245	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6678365	0.85[CEU][hapmap]
rs6683052	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6685475	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6685557	0.85[CEU][hapmap]
rs6690568	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	0.85[CEU][hapmap]
rs6693372	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6693884	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6694960	0.85[CEU][hapmap]
rs6696053	0.85[CEU][hapmap]
rs6700366	0.85[CEU][hapmap]
rs6702314	0.90[EUR][1000 genomes]
rs6702430	0.89[EUR][1000 genomes]
rs6703104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7331	0.85[CEU][hapmap]
rs7412088	0.86[CEU][hapmap]
rs7530328	0.85[CEU][hapmap]
rs7533551	0.85[CEU][hapmap]
rs7535882	0.85[CEU][hapmap]
rs7543197	0.86[CEU][hapmap]
rs7547642	0.87[CEU][hapmap]
rs7549063	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7551783	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555491	0.87[CEU][hapmap];0.96[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653522	MARK1	cis	parietal	SCAN
rs4653522	TGFB2	cis	cerebellum	SCAN

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	chr1:223856000-223858200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:223856800-223858200	Weak transcription	HMEC	breast
6	chr1:223856800-223862200	Weak transcription	Pancreas	Pancrea
7	chr1:223857000-223858200	Weak transcription	Stomach Mucosa	stomach
8	chr1:223857000-223858800	Weak transcription	Colonic Mucosa	Colon
9	chr1:223857400-223859400	Enhancers	NHDF-Ad	bronchial
10	chr1:223858000-223858600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links