Variant report

Variant	rs1898152
Chromosome Location	chr1:242292690-242292691
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	RAD21	chr1:242292443-242292869	MCF-7	breast:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
2	CTCF	chr1:242292516-242292731	K562	blood:	n/a	chr1:242292611-242292632
3	CTCF	chr1:242292369-242292846	HCT-116	colon:	n/a	chr1:242292611-242292632
4	CTCF	chr1:242292376-242292872	MCF-7	breast:	n/a	chr1:242292611-242292632
5	RAD21	chr1:242292366-242292850	HCT-116	colon:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
6	RAD21	chr1:242292370-242292857	A549	lung:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
7	CTCF	chr1:242292600-242292750	RPTEC	kidney:	n/a	chr1:242292611-242292632
8	RAD21	chr1:242292539-242292700	A549	lung:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
9	RAD21	chr1:242292325-242292856	HCT-116	colon:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
10	CTCF	chr1:242292424-242292797	GM12878	blood:	n/a	chr1:242292611-242292632
11	ZNF143	chr1:242292475-242292778	GM12878	blood:	n/a	n/a
12	CTCF	chr1:242292560-242292710	WERI-Rb-1	eye:	n/a	chr1:242292611-242292632
13	CTCF	chr1:242292425-242292779	MCF-7	breast:	n/a	chr1:242292611-242292632
14	FOXA1	chr1:242292508-242292745	T-47D	breast:	n/a	n/a
15	CTCF	chr1:242292491-242292739	Gliobla	brain:	n/a	chr1:242292611-242292632
16	CTCF	chr1:242292560-242292710	GM12865	blood:	n/a	chr1:242292611-242292632
17	CTCF	chr1:242292580-242292730	GM12873	blood:	n/a	chr1:242292611-242292632
18	ATF1	chr1:242292439-242292709	K562	blood:	n/a	n/a
19	CTCF	chr1:242292529-242292728	Hela-S3	cervix:	n/a	chr1:242292611-242292632
20	RAD21	chr1:242292327-242292925	MCF-7	breast:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
21	CTCF	chr1:242292547-242292709	HepG2	liver:	n/a	chr1:242292611-242292632
22	CTCF	chr1:242292540-242292690	HEK293	kidney:	n/a	chr1:242292611-242292632
23	CTCF	chr1:242292540-242292690	GM12865	blood:	n/a	chr1:242292611-242292632
24	ATF2	chr1:242292342-242292767	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr1:242292560-242292710	HMF	breast:	n/a	chr1:242292611-242292632
26	CTCF	chr1:242292560-242292710	GM12871	blood:	n/a	chr1:242292611-242292632
27	SMC3	chr1:242292433-242292718	GM12878	blood:	n/a	n/a
28	CTCF	chr1:242292506-242292722	GM12878	blood:	n/a	chr1:242292611-242292632
29	CTCF	chr1:242292560-242292710	GM12866	blood:	n/a	chr1:242292611-242292632
30	CTCF	chr1:242292442-242292740	K562	blood:	n/a	chr1:242292611-242292632
31	RAD21	chr1:242292448-242292726	SK-N-SH_RA	brain:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
32	CTCF	chr1:242292540-242292690	K562	blood:	n/a	chr1:242292611-242292632
33	CTCF	chr1:242292540-242292690	BE2_C	brain:	n/a	chr1:242292611-242292632
34	RAD21	chr1:242292394-242292802	H1-hESC	embryonic stem cell:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
35	CTCF	chr1:242292499-242292734	LNCaP	prostate:	n/a	chr1:242292611-242292632
36	CTCF	chr1:242292560-242292710	GM12869	blood:	n/a	chr1:242292611-242292632
37	CTCF	chr1:242292540-242292690	GM12878	blood:	n/a	chr1:242292611-242292632
38	RAD21	chr1:242292470-242292699	SK-N-SH_RA	brain:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
39	CTCF	chr1:242292580-242292730	Caco-2	colon:	n/a	chr1:242292611-242292632
40	CTCF	chr1:242292512-242292712	LNCaP	prostate:	n/a	chr1:242292611-242292632
41	CTCF	chr1:242292540-242292690	GM12868	blood:	n/a	chr1:242292611-242292632
42	RAD21	chr1:242292467-242292746	HepG2	liver:	n/a	chr1:242292614-242292633 chr1:242292616-242292628
43	CTCF	chr1:242292620-242292770	GM12871	blood:	n/a	n/a
44	CTCF	chr1:242292600-242292750	GM12874	blood:	n/a	chr1:242292611-242292632
45	MYC	chr1:242292532-242292768	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr1:242292540-242292690	HEEpiC	esophagus:	n/a	chr1:242292611-242292632
47	CTCF	chr1:242292540-242292690	SK-N-SH_RA	brain:	n/a	chr1:242292611-242292632
48	CTCF	chr1:242292540-242292690	Caco-2	colon:	n/a	chr1:242292611-242292632
49	CTCF	chr1:242292551-242292691	SK-N-SH_RA	brain:	n/a	chr1:242292611-242292632
50	FOS	chr1:242292467-242292690	MCF10A-Er-Src	breast:	n/a	chr1:242292678-242292686 chr1:242292678-242292685

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:242286116..242287870-chr1:242290000..242292729,2	K562	blood:
2	chr1:242182508..242183674-chr1:242292156..242293080,6	MCF-7	breast:

Variant related genes	Relation type
RNA5SP81	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1435952	0.82[ASN][1000 genomes]
rs1595120	0.82[ASN][1000 genomes]
rs1898154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636253	0.82[ASN][1000 genomes]
rs2636254	0.82[ASN][1000 genomes]
rs2800756	0.82[ASN][1000 genomes]
rs2800757	0.82[ASN][1000 genomes]
rs2840615	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2840616	0.82[ASN][1000 genomes]
rs316823	0.86[MKK][hapmap]
rs4658620	0.80[ASN][1000 genomes]
rs6663723	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv468672	chr1:242201247-242555949	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv470788	chr1:242201247-242555949	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv549462	chr1:242201247-242555949	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv528016	chr1:242223399-242451350	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv549463	chr1:242265419-242856854	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv998804	chr1:242281003-242491362	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1898152	FMN2	cis	parietal	SCAN
rs1898152	OPN3	cis	cerebellum	SCAN
rs1898152	PLD5	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242282200-242298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:242292600-242295800	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links