Variant report

Variant	rs1889316
Chromosome Location	chr1:154352017-154352018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:154351880-154352030	HepG2	liver:	n/a	n/a
2	RAD21	chr1:154351827-154352122	HepG2	liver:	n/a	n/a
3	CTCF	chr1:154351834-154352061	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:154351851-154352093	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:154352008-154352058	HCPEpiC	choroid plexus:	n/a
2	chr1:154352008-154352058	HUVEC	blood vessel:	n/a
3	chr1:154352008-154352058	HPAEpiC	pulmonary alveolar:	n/a
4	chr1:154352008-154352058	HL-60	blood:	n/a
5	chr1:154352008-154352058	PANC-1	pancreas:	n/a
6	chr1:154352008-154352058	HIPEpiC	eye:	n/a
7	chr1:154352008-154352058	AoSMC	blood vessel:	n/a
8	chr1:154352008-154352058	HAEpiC	amniotic membrane:	n/a
9	chr1:154352008-154352058	LNCaP	prostate:	n/a
10	chr1:154352008-154352058	HCM	heart:	n/a
11	chr1:154352008-154352058	SAEC	small airway:	n/a
12	chr1:154352008-154352058	GM19239	blood:	n/a
13	chr1:154352008-154352058	HNPCEpiC	eye:	n/a
14	chr1:154352008-154352058	BE2_C	brain:	n/a
15	chr1:154352008-154352058	Caco-2	colon:	n/a
16	chr1:154352008-154352058	SK-N-SH	brain:	n/a
17	chr1:154352008-154352058	MCF-7	breast:	n/a
18	chr1:154352008-154352058	NH-A	brain:	n/a
19	chr1:154352008-154352058	RPTEC	kidney:	n/a
20	chr1:154352008-154352058	AG09309	skin:	n/a
21	chr1:154352008-154352058	HepG2	liver:	n/a
22	chr1:154352008-154352058	Jurkat	blood:	n/a
23	chr1:154352008-154352058	NHDF-neo	bronchial:	n/a
24	chr1:154352008-154352058	GM06990	blood:	n/a
25	chr1:154352008-154352058	CMK	blood:	n/a
26	chr1:154352008-154352058	AG04450	lung:	fetal
27	chr1:154352008-154352058	MCF10A-Er-Src	breast:	n/a
28	chr1:154352008-154352058	A549	lung:	n/a
29	chr1:154352008-154352058	HMEC	breast:	n/a
30	chr1:154352008-154352058	Hepatocyte	liver:	n/a
31	chr1:154352008-154352058	HCF	heart:	n/a
32	chr1:154352008-154352058	HRCEpiC	kidney:	n/a
33	chr1:154352008-154352058	AG10803	skin:	n/a
34	chr1:154352008-154352058	BJ	skin:	n/a
35	chr1:154352008-154352058	NHBE	bronchial:	n/a
36	chr1:154352008-154352058	IMR90	lung:	fetal
37	chr1:154352008-154352058	HCT-116	colon:	n/a
38	chr1:154352008-154352058	K562	blood:	n/a
39	chr1:154352008-154352058	SK-N-SH_RA	brain:	n/a
40	chr1:154352008-154352058	SK-N-MC	brain:	n/a
41	chr1:154352008-154352058	U87	brain:	n/a
42	chr1:154352008-154352058	NB4	blood:	n/a
43	chr1:154352008-154352058	HEK293	kidney:	embryo
44	chr1:154352008-154352058	GM12892	blood:	n/a
45	chr1:154352008-154352058	NT2-D1	testis:	n/a
46	chr1:154352008-154352058	SKMC	muscle:	n/a
47	chr1:154352008-154352058	HRE	kidney:	n/a
48	chr1:154352008-154352058	HEEpiC	esophagus:	n/a
49	chr1:154352008-154352058	PFSK-1	brain:	n/a
50	chr1:154352008-154352058	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000237920	TF binding region
ENSG00000226855	TF binding region
ENSG00000237920	CpG island
ENSG00000226855	CpG island

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11265594	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12058332	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12063437	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12066892	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12068128	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12729561	0.85[EUR][1000 genomes]
rs12749618	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16865579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1948143	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28410194	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28530583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34065906	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34146123	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34749203	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34880256	0.89[EUR][1000 genomes]
rs34968830	0.90[EUR][1000 genomes]
rs35091500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35112510	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35229198	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35595831	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35629421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36029470	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3811451	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811452	0.91[EUR][1000 genomes]
rs4304577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4406622	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4414034	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4622059	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56023096	0.82[EUR][1000 genomes]
rs61803412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61803414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61804488	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61804489	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61812565	0.86[EUR][1000 genomes]
rs6662003	0.84[EUR][1000 genomes]
rs6662855	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663105	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666888	0.81[EUR][1000 genomes]
rs6667225	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672627	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686621	0.86[EUR][1000 genomes]
rs6690468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701309	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68031662	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68138282	0.85[EUR][1000 genomes]
rs749966	0.91[EUR][1000 genomes]
rs7511806	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518394	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523399	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530735	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530868	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552370	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9727988	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9728024	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9787014	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154326800-154360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:154351800-154352800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links