Variant report

Variant	rs12403890
Chromosome Location	chr1:171196138-171196139
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	chr1:171195986-171196214	GM10248	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
2	CTCF	chr1:171196000-171196150	AG09319	gingival:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
3	CTCF	chr1:171195975-171196225	Hela-S3	cervix:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
4	CTCF	chr1:171196000-171196150	Hela-S3	cervix:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
5	ZNF143	chr1:171195896-171196261	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr1:171195919-171196264	HepG2	liver:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
7	CTCF	chr1:171196060-171196210	BE2_C	brain:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
8	CTCF	chr1:171195713-171196364	HCT-116	colon:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
9	CTCF	chr1:171195967-171196221	LNCaP	prostate:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
10	CTCF	chr1:171196100-171196250	HCM	heart:	n/a	chr1:171196100-171196107
11	RAD21	chr1:171195847-171196335	HepG2	liver:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
12	CTCF	chr1:171196080-171196230	HAc	cerebellar:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
13	CTCF	chr1:171195940-171196286	K562	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
14	CTCF	chr1:171196020-171196170	WERI-Rb-1	eye:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
15	CTCF	chr1:171196000-171196150	HPF	lung:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
16	CTCF	chr1:171195962-171196266	HUVEC	blood vessel:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
17	CTCF	chr1:171195974-171196210	Fibrobl	skin:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
18	CTCF	chr1:171195964-171196214	NHEK	skin:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
19	CTCF	chr1:171196040-171196190	BE2_C	brain:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
20	CTCF	chr1:171196020-171196170	Caco-2	colon:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
21	RAD21	chr1:171195840-171196320	ECC-1	luminal epithelium:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
22	SMC3	chr1:171195937-171196255	K562	blood:	n/a	chr1:171196095-171196109
23	CTCF	chr1:171196060-171196210	GM12870	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
24	CTCF	chr1:171196020-171196170	NHDF-neo	bronchial:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
25	CTCF	chr1:171195979-171196225	Spleen_OC	spleen:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
26	CTCF	chr1:171195723-171196573	SK-N-SH	brain:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
27	CTCF	chr1:171196000-171196150	HMEC	breast:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
28	CTCF	chr1:171196040-171196190	RPTEC	kidney:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
29	CTCF	chr1:171196020-171196170	AG09319	gingival:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
30	CTCF	chr1:171195980-171196151	SK-N-SH_RA	brain:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
31	CTCF	chr1:171196080-171196230	HFF-Myc	foreskin:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
32	RAD21	chr1:171195707-171196513	SK-N-SH	brain:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
33	MAZ	chr1:171195943-171196211	GM12878	blood:	n/a	n/a
34	CTCF	chr1:171195954-171196258	Medullo	brain:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
35	CTCF	chr1:171196000-171196150	GM12865	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
36	CTCF	chr1:171196020-171196170	HBMEC	blood vessel:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
37	CTCF	chr1:171195980-171196216	ProgFib	skin:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
38	CTCF	chr1:171196040-171196190	HVMF	connective:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
39	RAD21	chr1:171195702-171196353	MCF-7	breast:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
40	CTCF	chr1:171195973-171196278	A549	lung:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
41	RAD21	chr1:171195870-171196316	IMR90	lung:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
42	CTCF	chr1:171195967-171196275	A549	lung:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
43	CTCF	chr1:171196060-171196210	K562	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
44	CTCF	chr1:171196000-171196150	GM12864	blood:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
45	RAD21	chr1:171195868-171196241	GM12878	blood:	n/a	chr1:171196091-171196110 chr1:171196100-171196109
46	SMC3	chr1:171195736-171196269	GM12878	blood:	n/a	chr1:171196095-171196109
47	CTCF	chr1:171196015-171196163	MCF-7	breast:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
48	CTCF	chr1:171196020-171196170	HepG2	liver:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
49	CTCF	chr1:171196080-171196230	A549	lung:	n/a	chr1:171196100-171196107 chr1:171196088-171196109
50	CTCF	chr1:171196040-171196190	MCF-7	breast:	n/a	chr1:171196100-171196107 chr1:171196088-171196109

No.	Distal block	Cell Line	Cell type
1	chr1:171050311..171050975-chr1:171195652..171196489,2	MCF-7	breast:
2	chr1:171195796..171196545-chr1:171282426..171283362,2	MCF-7	breast:
3	chr1:171050144..171051119-chr1:171195616..171196435,6	MCF-7	breast:
4	chr1:170935633..170937000-chr1:171195928..171196554,4	MCF-7	breast:
5	chr1:171051388..171052230-chr1:171195968..171196512,2	MCF-7	breast:
6	chr1:170935902..170936885-chr1:171195525..171196580,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225243	TF binding region
ENSG00000076258	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10912616	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065544	0.97[ASN][1000 genomes]
rs12402732	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12720462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16864174	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864177	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864194	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987921	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1987944	1.00[ASN][1000 genomes]
rs2020863	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049920	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064077	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2072755	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075988	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2103537	0.82[ASN][1000 genomes]
rs2179106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369891	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28369914	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3861947	0.97[ASN][1000 genomes]
rs4073692	0.84[ASN][1000 genomes]
rs4073693	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4622096	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4631734	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56370691	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57305992	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815363	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61815421	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815423	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815424	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815425	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815427	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714167	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535210	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551934	0.96[AMR][1000 genomes];0.99[ASN][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171191400-171197200	Weak transcription	Fetal Kidney	kidney
2	chr1:171194200-171200400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:171196000-171199000	Weak transcription	Fetal Lung	lung

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