Variant report

Variant	rs543743758
Chromosome Location	chr1:247276595-247276596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:247276296-247276978	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:247276027-247276608	HepG2	liver:	n/a	n/a
3	MYC	chr1:247276525-247276783	MCF10A-Er-Src	breast:	n/a	n/a
4	BRCA1	chr1:247276484-247276640	HepG2	liver:	n/a	n/a
5	MAX	chr1:247276512-247277094	HepG2	liver:	n/a	n/a
6	BACH1	chr1:247276594-247276742	H1-hESC	embryonic stem cell:	n/a	n/a
7	NR3C1	chr1:247276464-247276771	ECC-1	luminal epithelium:	n/a	n/a
8	SIN3AK20	chr1:247276389-247276609	HepG2	liver:	n/a	n/a
9	JUND	chr1:247276371-247276722	HepG2	liver:	n/a	n/a
10	TEAD4	chr1:247276371-247276843	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:247276312-247276662	HepG2	liver:	n/a	n/a
12	CTCF	chr1:247276460-247276610	HepG2	liver:	n/a	chr1:247276521-247276537 chr1:247276520-247276538 chr1:247276515-247276536
13	ARID3A	chr1:247275900-247276723	HepG2	liver:	n/a	n/a
14	RAD21	chr1:247276396-247276665	HepG2	liver:	n/a	chr1:247276425-247276435 chr1:247276518-247276537 chr1:247276409-247276416 chr1:247276520-247276532
15	CEBPD	chr1:247276327-247276598	HepG2	liver:	n/a	n/a
16	ESR1	chr1:247276363-247276761	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr1:247276240-247277067	ECC-1	luminal epithelium:	n/a	n/a
18	MYC	chr1:247276568-247276702	MCF10A-Er-Src	breast:	n/a	n/a
19	MXI1	chr1:247276343-247277061	HepG2	liver:	n/a	n/a
20	STAT3	chr1:247276545-247276789	MCF10A-Er-Src	breast:	n/a	n/a
21	MAFF	chr1:247276460-247276736	HepG2	liver:	n/a	n/a
22	RCOR1	chr1:247276408-247276824	HepG2	liver:	n/a	n/a
23	BHLHE40	chr1:247276350-247276737	HepG2	liver:	n/a	n/a
24	ESR1	chr1:247276344-247276830	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr1:247274450-247277052	HepG2	liver:	n/a	n/a
26	MAFK	chr1:247276414-247276625	HepG2	liver:	n/a	n/a
27	TCF12	chr1:247276307-247277095	ECC-1	luminal epithelium:	n/a	n/a
28	JUN	chr1:247276457-247276700	HepG2	liver:	n/a	chr1:247276555-247276568
29	FOS	chr1:247276517-247276723	MCF10A-Er-Src	breast:	n/a	n/a
30	ZBTB7A	chr1:247276322-247276655	HepG2	liver:	n/a	n/a
31	MYBL2	chr1:247276390-247276783	HepG2	liver:	n/a	n/a
32	TBP	chr1:247276322-247276771	HepG2	liver:	n/a	n/a
33	RXRA	chr1:247276396-247276698	HepG2	liver:	n/a	chr1:247276523-247276530
34	MYC	chr1:247276578-247276596	HepG2	liver:	n/a	n/a
35	STAT3	chr1:247276476-247276783	MCF10A-Er-Src	breast:	n/a	n/a
36	MAFK	chr1:247276478-247276678	HepG2	liver:	n/a	n/a
37	RFX5	chr1:247276439-247276701	HepG2	liver:	n/a	n/a
38	SMC3	chr1:247276379-247276678	HepG2	liver:	n/a	chr1:247276522-247276536
39	ZBTB7A	chr1:247276295-247276897	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:247276349-247276737	HepG2	liver:	n/a	n/a
41	MAX	chr1:247276348-247276942	ECC-1	luminal epithelium:	n/a	n/a
42	ESR1	chr1:247276388-247276900	ECC-1	luminal epithelium:	n/a	n/a
43	HEY1	chr1:247276304-247276763	HepG2	liver:	n/a	n/a
44	JUND	chr1:247276415-247276696	HepG2	liver:	n/a	n/a
45	MYBL2	chr1:247276268-247277036	HepG2	liver:	n/a	n/a
46	MAZ	chr1:247276197-247276695	HepG2	liver:	n/a	n/a
47	TCF12	chr1:247276304-247276842	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247276552-247276602	SK-N-SH	brain:	n/a
2	chr1:247276552-247276602	CMK	blood:	n/a
3	chr1:247276552-247276602	HCM	heart:	n/a
4	chr1:247276552-247276602	BJ	skin:	n/a
5	chr1:247276552-247276602	Caco-2	colon:	n/a
6	chr1:247276552-247276602	U87	brain:	n/a
7	chr1:247276552-247276602	NHDF-neo	bronchial:	n/a
8	chr1:247276552-247276602	HAEpiC	amniotic membrane:	n/a
9	chr1:247276552-247276602	GM12892	blood:	n/a
10	chr1:247276552-247276602	HEEpiC	esophagus:	n/a
11	chr1:247276552-247276602	HCPEpiC	choroid plexus:	n/a
12	chr1:247276552-247276602	HRE	kidney:	n/a
13	chr1:247276552-247276602	HRPEpiC	eye:	n/a
14	chr1:247276552-247276602	AG09309	skin:	n/a
15	chr1:247276552-247276602	NT2-D1	testis:	n/a
16	chr1:247276552-247276602	MCF-7	breast:	n/a
17	chr1:247276552-247276602	AG09319	gingival:	n/a
18	chr1:247276552-247276602	NB4	blood:	n/a
19	chr1:247276552-247276602	PFSK-1	brain:	n/a
20	chr1:247276552-247276602	SKMC	muscle:	n/a
21	chr1:247276552-247276602	HMEC	breast:	n/a
22	chr1:247276552-247276602	AG04450	lung:	fetal
23	chr1:247276552-247276602	IMR90	lung:	fetal
24	chr1:247276552-247276602	NHBE	bronchial:	n/a
25	chr1:247276552-247276602	GM12878	blood:	n/a
26	chr1:247276552-247276602	ProgFib	skin:	n/a
27	chr1:247276552-247276602	LNCaP	prostate:	n/a
28	chr1:247276552-247276602	MCF10A-Er-Src	breast:	n/a
29	chr1:247276552-247276602	GM06990	blood:	n/a
30	chr1:247276552-247276602	HIPEpiC	eye:	n/a
31	chr1:247276552-247276602	HCT-116	colon:	n/a
32	chr1:247276552-247276602	Hepatocyte	liver:	n/a
33	chr1:247276552-247276602	SK-N-SH_RA	brain:	n/a
34	chr1:247276552-247276602	GM19239	blood:	n/a
35	chr1:247276552-247276602	HEK293	kidney:	embryo
36	chr1:247276552-247276602	HUVEC	blood vessel:	n/a
37	chr1:247276552-247276602	AG10803	skin:	n/a
38	chr1:247276552-247276602	AG04449	skin:	fetal
39	chr1:247276552-247276602	HL-60	blood:	n/a
40	chr1:247276552-247276602	K562	blood:	n/a
41	chr1:247276552-247276602	Hela-S3	cervix:	n/a
42	chr1:247276552-247276602	HCF	heart:	n/a
43	chr1:247276552-247276602	PrEC	prostate:	n/a
44	chr1:247276552-247276602	HRCEpiC	kidney:	n/a
45	chr1:247276552-247276602	ECC-1	luminal epithelium:	n/a
46	chr1:247276552-247276602	ovcar-3	ovarian:	n/a
47	chr1:247276552-247276602	AoSMC	blood vessel:	n/a
48	chr1:247276552-247276602	HepG2	liver:	n/a
49	chr1:247276552-247276602	SAEC	small airway:	n/a
50	chr1:247276552-247276602	RPTEC	kidney:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
2	chr1:247276067..247278651-chr1:247493890..247496062,2	MCF-7	breast:
3	chr1:247261271..247263933-chr1:247276366..247278097,2	K562	blood:
4	chr1:247092146..247096759-chr1:247274350..247278356,6	MCF-7	breast:
5	chr1:247262370..247270931-chr1:247272613..247278774,19	MCF-7	breast:
6	chr1:247275409..247277041-chr1:247418740..247421372,2	K562	blood:

No data

Variant related genes	Relation type
C1orf229	TF binding region
C1orf229	CpG island
ENSG00000227671	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000153207	Chromatin interaction
ENSG00000188295	Chromatin interaction
ENSG00000197617	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
8	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
12	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1014012	chr1:247207932-247289138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
20	nsv873429	chr1:247230809-247288469	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv549547	chr1:247233156-247281769	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv873430	chr1:247233156-247291400	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv873431	chr1:247242836-247297502	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
25	esv3343320	chr1:247274154-247276702	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
26	nsv549548	chr1:247274439-247278707	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
27	nsv549549	chr1:247275215-247293214	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247275600-247276600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:247275600-247276600	Enhancers	Fetal Heart	heart
3	chr1:247275600-247276800	Enhancers	Spleen	Spleen
4	chr1:247275600-247276800	Enhancers	HMEC	breast
5	chr1:247275600-247279200	Flanking Active TSS	HepG2	liver
6	chr1:247275800-247276600	Enhancers	Lung	lung
7	chr1:247275800-247276800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:247275800-247276800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:247275800-247277000	Enhancers	Liver	Liver
10	chr1:247276000-247276600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:247276000-247276600	Enhancers	K562	blood
12	chr1:247276000-247276600	Enhancers	NHEK	skin
13	chr1:247276000-247276600	Enhancers	Osteobl	bone
14	chr1:247276000-247276800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:247276000-247276800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:247276000-247276800	Enhancers	Adipose Nuclei	Adipose
17	chr1:247276000-247276800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr1:247276000-247276800	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr1:247276000-247276800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:247276000-247276800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:247276000-247277000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr1:247276000-247278400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:247276200-247276800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:247276200-247277000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:247276200-247277000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:247276200-247277200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:247276400-247276600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:247276400-247276600	Enhancers	Right Ventricle	heart
29	chr1:247276400-247276800	Enhancers	Gastric	stomach
30	chr1:247276400-247276800	Weak transcription	Pancreas	Pancrea
31	chr1:247276400-247276800	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links