Variant report

Variant	rs61523335
Chromosome Location	chr1:93487128-93487129
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	chr1:93486758-93487621	SK-N-SH	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
2	CTCF	chr1:93487087-93487542	GM12878	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
3	RAD21	chr1:93487072-93487491	GM12878	blood:	n/a	n/a
4	CTCF	chr1:93486973-93487646	HCT-116	colon:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
5	RAD21	chr1:93487036-93487577	ECC-1	luminal epithelium:	n/a	n/a
6	RAD21	chr1:93487114-93487537	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr1:93487093-93487478	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr1:93487117-93487537	GM12878	blood:	n/a	n/a
9	STAT3	chr1:93486918-93487360	MCF10A-Er-Src	breast:	n/a	n/a
10	SMC3	chr1:93486859-93487534	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr1:93487094-93487474	A549	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
12	CTCF	chr1:93487003-93487450	Medullo	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
13	SMC3	chr1:93487115-93487511	HepG2	liver:	n/a	n/a
14	RAD21	chr1:93487047-93487574	A549	lung:	n/a	n/a
15	CTCF	chr1:93487126-93487131	GM10266	blood:	n/a	n/a
16	CTCF	chr1:93487083-93487504	K562	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
17	RAD21	chr1:93486875-93487832	SK-N-SH	brain:	n/a	n/a
18	ZNF143	chr1:93487120-93487492	GM12878	blood:	n/a	n/a
19	RAD21	chr1:93487103-93487530	SK-N-SH_RA	brain:	n/a	n/a
20	RAD21	chr1:93487048-93487563	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr1:93487095-93487528	IMR90	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
22	RAD21	chr1:93487061-93487494	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr1:93487121-93487495	K562	blood:	n/a	n/a
24	RAD21	chr1:93487111-93487504	SK-N-SH_RA	brain:	n/a	n/a
25	SMC3	chr1:93487108-93487527	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr1:93487116-93487532	HepG2	liver:	n/a	n/a
27	RAD21	chr1:93486956-93487690	HCT-116	colon:	n/a	n/a
28	CTCF	chr1:93487056-93487500	HepG2	liver:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
29	RAD21	chr1:93487106-93487505	HepG2	liver:	n/a	n/a
30	RAD21	chr1:93487064-93487581	A549	lung:	n/a	n/a
31	SMC3	chr1:93487087-93487599	GM12878	blood:	n/a	n/a
32	CTCF	chr1:93487058-93487499	A549	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
33	CTCF	chr1:93487091-93487517	K562	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
34	RAD21	chr1:93487102-93487528	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr1:93487068-93487553	MCF-7	breast:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
36	RAD21	chr1:93487018-93487567	HepG2	liver:	n/a	n/a
37	RAD21	chr1:93487012-93487633	HCT-116	colon:	n/a	n/a
38	CTCF	chr1:93486931-93487685	A549	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
39	RAD21	chr1:93487087-93487604	MCF-7	breast:	n/a	n/a
40	RAD21	chr1:93487039-93487507	MCF-7	breast:	n/a	n/a
41	CTCF	chr1:93487090-93487488	H1-hESC	embryonic stem cell:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
42	CTCF	chr1:93487124-93487407	ECC-1	luminal epithelium:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
43	RAD21	chr1:93487126-93487502	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93485980..93488495-chr1:93489742..93491453,2	K562	blood:
2	chr1:93486773..93487911-chr1:93527469..93528398,9	K562	blood:
3	chr1:93486837..93487799-chr1:94374760..94375360,2	K562	blood:
4	chr1:93485808..93487588-chr1:93526047..93528280,2	MCF-7	breast:
5	chr1:93486832..93487777-chr1:93527684..93528337,5	MCF-7	breast:
6	chr1:93324004..93325373-chr1:93486850..93487700,5	K562	blood:

Variant related genes	Relation type
RN7SKP123	TF binding region
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10874754	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164862	0.98[EUR][1000 genomes]
rs11164865	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590314	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12084977	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091867	0.99[EUR][1000 genomes]
rs12092136	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12094815	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2485031	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2785601	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs491699	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs569268	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57478994	0.85[AFR][1000 genomes]
rs59284207	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6657919	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6686863	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688632	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103530	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536849	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93474200-93490600	Weak transcription	K562	blood
2	chr1:93480400-93491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:93482200-93487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:93482600-93487400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:93486800-93494000	Enhancers	Dnd41	blood
6	chr1:93487000-93487600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:93487000-93487600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:93487000-93487600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:93487000-93487600	Enhancers	Liver	Liver

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