Variant report

Variant	rs1925714
Chromosome Location	chr1:228703289-228703290
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	CTCF	chr1:228702979-228703307	A549	lung:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
2	CTCF	chr1:228703003-228703307	HUVEC	blood vessel:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
3	CTCF	chr1:228703012-228703295	K562	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
4	CTCF	chr1:228702958-228703362	GM12878	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
5	CTCF	chr1:228703180-228703330	GM12874	blood:	n/a	n/a
6	RAD21	chr1:228702979-228703325	HepG2	liver:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
7	RAD21	chr1:228702810-228703476	HCT-116	colon:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
8	CTCF	chr1:228703038-228703293	Hela-S3	cervix:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
9	RAD21	chr1:228703009-228703374	ECC-1	luminal epithelium:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
10	RAD21	chr1:228702984-228703339	A549	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
11	CTCF	chr1:228703280-228703430	GM12866	blood:	n/a	n/a
12	CTCF	chr1:228703140-228703290	GM12871	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175
13	CTCF	chr1:228703007-228703360	Spleen_OC	spleen:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
14	RAD21	chr1:228702927-228703340	GM12878	blood:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
15	RAD21	chr1:228702901-228703303	GM12878	blood:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
16	JUND	chr1:228702942-228703301	K562	blood:	n/a	n/a
17	CTCF	chr1:228702910-228703401	K562	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
18	RAD21	chr1:228702850-228703417	H1-hESC	embryonic stem cell:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
19	RAD21	chr1:228702950-228703316	GM12878	blood:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
20	RAD21	chr1:228702928-228703328	SK-N-SH_RA	brain:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
21	CTCF	chr1:228703240-228703390	GM12872	blood:	n/a	n/a
22	RAD21	chr1:228702832-228703459	A549	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
23	CTCF	chr1:228702984-228703301	A549	lung:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
24	CTCF	chr1:228702899-228703451	MCF-7	breast:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
25	CTCF	chr1:228703049-228703298	MCF-7	breast:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
26	RAD21	chr1:228702868-228703411	H1-hESC	embryonic stem cell:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
27	CTCF	chr1:228702891-228703386	IMR90	lung:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
28	MAZ	chr1:228702991-228703305	K562	blood:	n/a	n/a
29	ZNF143	chr1:228702941-228703334	K562	blood:	n/a	chr1:228703084-228703103
30	RAD21	chr1:228702907-228703351	MCF-7	breast:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
31	RAD21	chr1:228702932-228703363	K562	blood:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
32	RAD21	chr1:228702762-228703474	HCT-116	colon:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
33	CTCF	chr1:228703044-228703307	Pancreas_OC	pancreas:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
34	RAD21	chr1:228702799-228703492	A549	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
35	CTCF	chr1:228703140-228703290	RPTEC	kidney:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175
36	CTCF	chr1:228702571-228703529	A549	lung:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
37	RAD21	chr1:228702946-228703371	H1-hESC	embryonic stem cell:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
38	RAD21	chr1:228703002-228703404	MCF-7	breast:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
39	CTCF	chr1:228703260-228703410	SAEC	small airway:	n/a	n/a
40	CTCF	chr1:228702981-228703292	H1-hESC	embryonic stem cell:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
41	CTCF	chr1:228702674-228703434	K562	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
42	CTCF	chr1:228702891-228703367	HepG2	liver:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
43	CTCF	chr1:228702968-228703291	HepG2	liver:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
44	RAD21	chr1:228702947-228703385	IMR90	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
45	CTCF	chr1:228703072-228703302	GM10248	blood:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703072-228703085
46	CTCF	chr1:228703140-228703290	HAc	cerebellar:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175
47	RFX5	chr1:228702990-228703311	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr1:228703055-228703303	Gliobla	brain:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
49	RAD21	chr1:228702875-228703407	ECC-1	luminal epithelium:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
50	GATA1	chr1:228699888-228703545	K562	blood:	n/a	chr1:228701158-228701168

No.	Distal block	Cell Line	Cell type
1	chr1:228651785..228653360-chr1:228701547..228703326,2	K562	blood:
2	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
3	chr1:228696529..228699343-chr1:228702490..228705353,2	K562	blood:
4	chr1:228191722..228192636-chr1:228703111..228703660,2	K562	blood:
5	chr1:228456017..228456963-chr1:228702685..228703640,2	K562	blood:
6	chr1:228659611..228660330-chr1:228702674..228703564,2	K562	blood:
7	chr1:228452377..228453300-chr1:228702937..228703662,2	K562	blood:
8	chr1:228392725..228394871-chr1:228701724..228704719,2	K562	blood:
9	chr1:228688493..228689315-chr1:228702705..228703594,3	MCF-7	breast:
10	chr1:228528158..228528703-chr1:228703089..228703660,2	K562	blood:
11	chr1:228414817..228415566-chr1:228702553..228703686,3	K562	blood:
12	chr1:228645121..228649502-chr1:228703257..228706050,4	MCF-7	breast:
13	chr1:228566384..228567022-chr1:228702609..228703392,3	MCF-7	breast:
14	chr1:228651267..228651991-chr1:228702700..228703388,2	K562	blood:
15	chr1:228353333..228353944-chr1:228702817..228703586,2	K562	blood:
16	chr1:228688334..228689291-chr1:228702696..228703587,3	K562	blood:
17	chr1:228400895..228401787-chr1:228702783..228703634,3	K562	blood:

Variant related genes	Relation type
BTNL10	TF binding region
ENSG00000181873	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000181201	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1007686	0.85[CEU][hapmap]
rs10753451	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753452	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799479	0.82[EUR][1000 genomes]
rs10916313	0.85[CEU][hapmap]
rs10916317	0.85[CEU][hapmap]
rs10916338	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12028431	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035708	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140890	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12407568	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12542	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1925717	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925721	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925722	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1925730	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2182200	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35598069	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35724040	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147255	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147256	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412590	0.83[EUR][1000 genomes]
rs4653551	0.85[CEU][hapmap]
rs4653554	0.84[EUR][1000 genomes]
rs4653558	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653966	0.84[EUR][1000 genomes]
rs4653968	0.82[EUR][1000 genomes]
rs4653969	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4653970	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4653977	0.93[ASN][1000 genomes]
rs4653979	0.95[ASN][1000 genomes]
rs4654723	0.80[MEX][hapmap]
rs6426503	0.85[CEU][hapmap]
rs6426505	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6426507	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6669744	0.82[EUR][1000 genomes]
rs6670856	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6678145	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs728964	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415895	1.00[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs744668	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524236	0.85[CEU][hapmap]
rs7529055	0.85[CEU][hapmap]
rs7533560	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
5	nsv549297	chr1:228681195-228720480	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv468305	chr1:228681195-228731677	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv549298	chr1:228681195-228731677	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947521	chr1:228698244-228704499	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Tuberculosis	24057671	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925714	WDR26	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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