Variant report

Variant	rs3753261
Chromosome Location	chr1:119910489-119910490
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	SMC3	chr1:119909929-119910569	HepG2	liver:	n/a	chr1:119910313-119910327
2	RAD21	chr1:119909914-119910537	HepG2	liver:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
3	RAD21	chr1:119909912-119910571	ECC-1	luminal epithelium:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
4	CTCF	chr1:119910191-119910498	A549	lung:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
5	SMC3	chr1:119909971-119910566	Hela-S3	cervix:	n/a	chr1:119910313-119910327
6	RAD21	chr1:119909840-119910790	SK-N-SH	brain:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
7	NFYB	chr1:119910191-119910590	GM12878	blood:	n/a	chr1:119910356-119910371 chr1:119910361-119910371 chr1:119910361-119910371
8	RAD21	chr1:119910087-119910497	SK-N-SH_RA	brain:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
9	CTCF	chr1:119910037-119910534	HepG2	liver:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
10	ZNF143	chr1:119910136-119910511	GM12878	blood:	n/a	n/a
11	JUND	chr1:119910175-119910497	H1-hESC	embryonic stem cell:	n/a	chr1:119910363-119910372
12	CTCF	chr1:119910115-119910565	IMR90	lung:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
13	CTCF	chr1:119910036-119910616	MCF-7	breast:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
14	RAD21	chr1:119909943-119910494	H1-hESC	embryonic stem cell:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
15	RAD21	chr1:119910127-119910542	ECC-1	luminal epithelium:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
16	RAD21	chr1:119910013-119910531	SK-N-SH_RA	brain:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
17	CTCF	chr1:119910340-119910490	HFF-Myc	foreskin:	n/a	n/a
18	SMC3	chr1:119909877-119910541	GM12878	blood:	n/a	chr1:119910313-119910327
19	RAD21	chr1:119910034-119910519	IMR90	lung:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
20	RAD21	chr1:119909965-119910529	HepG2	liver:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
21	RAD21	chr1:119910070-119910496	GM12878	blood:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
22	FOS	chr1:119910237-119910536	MCF10A-Er-Src	breast:	n/a	chr1:119910363-119910372
23	CTCF	chr1:119910022-119910524	MCF-7	breast:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
24	ZNF143	chr1:119910145-119910508	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr1:119909985-119910527	Hela-S3	cervix:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
26	CTCF	chr1:119910118-119910513	HCT-116	colon:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
27	RAD21	chr1:119910029-119910572	A549	lung:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
28	CTCF	chr1:119910220-119910490	HFF	foreskin:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
29	RAD21	chr1:119910010-119910530	GM12878	blood:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
30	NFYB	chr1:119910218-119910568	K562	blood:	n/a	chr1:119910356-119910371 chr1:119910361-119910371 chr1:119910361-119910371
31	CTCF	chr1:119909822-119910740	SK-N-SH	brain:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
32	CTCF	chr1:119910066-119910586	HCT-116	colon:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
33	CTCF	chr1:119910340-119910490	HCT-116	colon:	n/a	n/a
34	RAD21	chr1:119910042-119910587	H1-hESC	embryonic stem cell:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
35	CTCF	chr1:119910360-119910510	WI-38	lung:	n/a	n/a
36	RAD21	chr1:119909983-119910595	HCT-116	colon:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
37	RAD21	chr1:119909920-119910575	HCT-116	colon:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
38	RAD21	chr1:119909884-119910527	H1-hESC	embryonic stem cell:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
39	NFYB	chr1:119910199-119910558	Hela-S3	cervix:	n/a	chr1:119910356-119910371 chr1:119910361-119910371 chr1:119910361-119910371
40	MAFK	chr1:119910201-119910510	H1-hESC	embryonic stem cell:	n/a	chr1:119910407-119910418
41	CTCF	chr1:119910062-119910639	A549	lung:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
42	CTCF	chr1:119910091-119910531	K562	blood:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
43	CTCF	chr1:119910023-119910560	GM12878	blood:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
44	CTCF	chr1:119910054-119910537	H1-hESC	embryonic stem cell:	n/a	chr1:119910311-119910329 chr1:119910316-119910324 chr1:119910306-119910327
45	RAD21	chr1:119910127-119910512	K562	blood:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
46	RAD21	chr1:119909909-119910603	MCF-7	breast:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
47	RAD21	chr1:119910127-119910510	A549	lung:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
48	RAD21	chr1:119909877-119910527	HepG2	liver:	n/a	chr1:119910319-119910326 chr1:119910309-119910328
49	SMC3	chr1:119909904-119910647	SK-N-SH	brain:	n/a	chr1:119910313-119910327
50	RAD21	chr1:119910012-119910586	MCF-7	breast:	n/a	chr1:119910319-119910326 chr1:119910309-119910328

No.	Distal block	Cell Line	Cell type
1	chr1:119818904..119819557-chr1:119910123..119910771,2	MCF-7	breast:
2	chr1:119828910..119830613-chr1:119909189..119910809,25	MCF-7	breast:
3	chr1:118694047..118694604-chr1:119909841..119910884,3	K562	blood:
4	chr1:119828739..119830086-chr1:119909537..119910745,9	MCF-7	breast:

Variant related genes	Relation type
HAO2	TF binding region
HAO2-IT1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10923800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071883	1.00[YRI][hapmap]
rs3820030	0.93[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119903400-119911800	Enhancers	HepG2	liver
2	chr1:119906400-119914400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:119908200-119915400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:119908600-119911400	Enhancers	Liver	Liver
5	chr1:119910000-119910600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:119910000-119910800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:119910200-119910600	Enhancers	HMEC	breast
8	chr1:119910200-119911400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:119910400-119910600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:119910400-119910600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:119910400-119910600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:119910400-119910600	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links