Variant report

Variant	rs2525541
Chromosome Location	chr7:99547530-99547531
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	chr7:99547269-99547552	A549	lung:	n/a	chr7:99547422-99547436
2	CTCF	chr7:99547380-99547530	WERI-Rb-1	eye:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
3	CTCF	chr7:99547440-99547590	GM12878	blood:	n/a	n/a
4	RAD21	chr7:99547214-99547627	H1-hESC	embryonic stem cell:	n/a	chr7:99547422-99547436
5	CTCF	chr7:99547380-99547530	HRPEpiC	eye:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
6	CTCF	chr7:99547380-99547530	GM12873	blood:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
7	RAD21	chr7:99547152-99547719	HCT-116	colon:	n/a	chr7:99547422-99547436
8	CTCF	chr7:99547107-99547706	SK-N-SH	brain:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
9	ZNF143	chr7:99547360-99547560	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr7:99547294-99547576	IMR90	lung:	n/a	chr7:99547422-99547436
11	CTCF	chr7:99547380-99547530	GM06990	blood:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
12	RAD21	chr7:99547218-99547688	HCT-116	colon:	n/a	chr7:99547422-99547436
13	CTCF	chr7:99547330-99547553	Spleen_OC	spleen:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
14	MAFK	chr7:99547361-99547548	HepG2	liver:	n/a	n/a
15	CTCF	chr7:99547352-99547531	Hela-S3	cervix:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
16	RAD21	chr7:99547260-99547582	H1-hESC	embryonic stem cell:	n/a	chr7:99547422-99547436
17	CTCF	chr7:99547480-99547630	HEEpiC	esophagus:	n/a	n/a
18	CTCF	chr7:99547380-99547530	AG09319	gingival:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
19	RAD21	chr7:99547248-99547701	MCF-7	breast:	n/a	chr7:99547422-99547436
20	SMC3	chr7:99547245-99547609	HepG2	liver:	n/a	n/a
21	CTCF	chr7:99547310-99547557	HUVEC	blood vessel:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
22	CTCF	chr7:99547189-99547669	HCT-116	colon:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
23	CTCF	chr7:99547206-99547587	HCT-116	colon:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
24	CTCF	chr7:99547300-99547543	HepG2	liver:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
25	CTCF	chr7:99547380-99547530	HMEC	breast:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
26	CTCF	chr7:99547400-99547550	BE2_C	brain:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
27	CTCF	chr7:99547178-99547769	A549	lung:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
28	CTCF	chr7:99547208-99547604	HepG2	liver:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
29	CTCF	chr7:99547400-99547550	GM12871	blood:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
30	CTCF	chr7:99547380-99547530	HCM	heart:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
31	RAD21	chr7:99547094-99547764	SK-N-SH	brain:	n/a	chr7:99547422-99547436
32	SMC3	chr7:99547196-99547787	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr7:99547245-99547600	H1-hESC	embryonic stem cell:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
34	CTCF	chr7:99547285-99547606	A549	lung:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
35	CTCF	chr7:99547400-99547550	NHDF-neo	bronchial:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
36	RAD21	chr7:99547177-99547664	A549	lung:	n/a	chr7:99547422-99547436
37	RAD21	chr7:99547228-99547589	HepG2	liver:	n/a	chr7:99547422-99547436
38	RAD21	chr7:99547271-99547620	H1-hESC	embryonic stem cell:	n/a	chr7:99547422-99547436
39	CTCF	chr7:99547400-99547550	HVMF	connective:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
40	RAD21	chr7:99547258-99547537	SK-N-SH_RA	brain:	n/a	chr7:99547422-99547436
41	CTCF	chr7:99547380-99547530	SK-N-SH_RA	brain:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
42	CTCF	chr7:99547380-99547530	HFF	foreskin:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
43	CTCF	chr7:99547257-99547718	MCF-7	breast:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
44	RAD21	chr7:99547229-99547680	MCF-7	breast:	n/a	chr7:99547422-99547436
45	CTCF	chr7:99547270-99547595	GM12878	blood:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
46	RAD21	chr7:99547243-99547541	Hela-S3	cervix:	n/a	chr7:99547422-99547436
47	CTCF	chr7:99547170-99547713	MCF-7	breast:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
48	SMC3	chr7:99547286-99547623	GM12878	blood:	n/a	n/a
49	CTCF	chr7:99547380-99547530	Caco-2	colon:	n/a	chr7:99547422-99547435 chr7:99547420-99547438
50	CTCF	chr7:99547320-99547556	LNCaP	prostate:	n/a	chr7:99547422-99547435 chr7:99547420-99547438

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99510461..99511401-chr7:99546931..99547855,3	MCF-7	breast:
2	chr7:99546378..99548989-chr7:99551538..99554041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222966	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048705	0.85[CHB][hapmap]
rs10808114	0.85[CHB][hapmap]
rs1981548	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057766	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060452	0.84[CHB][hapmap]
rs2107351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247761	0.84[CHB][hapmap]
rs2525534	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525542	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525547	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527891	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527892	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527894	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527895	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527897	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527899	0.84[CHB][hapmap]
rs2527901	0.85[CHB][hapmap]
rs2527903	0.84[CHB][hapmap]
rs2527907	0.84[CHB][hapmap]
rs2527914	0.85[CHB][hapmap]
rs2527918	0.83[CHB][hapmap]
rs2527919	0.85[CHB][hapmap]
rs2527922	0.85[CHB][hapmap]
rs2571992	0.84[CHB][hapmap]
rs2571997	0.84[CHB][hapmap]
rs2571998	0.84[CHB][hapmap]
rs2572003	0.85[CHB][hapmap]
rs2572005	0.85[CHB][hapmap]
rs2572006	0.84[CHB][hapmap]
rs2572008	0.85[CHB][hapmap]
rs2572010	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv607930	chr7:99525241-99602191	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv1828362	chr7:99530233-99628773	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv888772	chr7:99533178-99602191	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1830255	chr7:99544908-99626331	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	esv1832985	chr7:99546856-99615911	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2525541	TRIM4	cis	normal skin	skin_eQTL
rs2525541	TRIM4	cis	Artery Aorta	GTEx
rs2525541	TRIM4	cis	Muscle Skeletal	GTEx
rs2525541	TRIM4	cis	Artery Tibial	GTEx
rs2525541	TRIM4	cis	Thyroid	GTEx
rs2525541	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2525541	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2525541	TRIM4	cis	multi-tissue	Pritchard
rs2525541	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2525541	TRIM4	cis	Stomach	GTEx
rs2525541	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2525541	TRIM4	cis	Nerve Tibial	GTEx
rs2525541	TRIM4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99532400-99548000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:99545800-99548000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:99546400-99552800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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