Variant report

Variant	rs6978458
Chromosome Location	chr7:48028664-48028665
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	chr7:48028484-48028695	MCF-7	breast:	n/a	chr7:48028571-48028580
2	CTCF	chr7:48028520-48028670	BE2_C	brain:	n/a	chr7:48028571-48028580
3	CTCF	chr7:48028419-48028725	K562	blood:	n/a	chr7:48028571-48028580
4	CTCF	chr7:48028499-48028687	ProgFib	skin:	n/a	chr7:48028571-48028580
5	CTCF	chr7:48028540-48028690	GM12864	blood:	n/a	chr7:48028571-48028580
6	CTCF	chr7:48028540-48028690	HEEpiC	esophagus:	n/a	chr7:48028571-48028580
7	CTCF	chr7:48028540-48028690	HCPEpiC	choroid plexus:	n/a	chr7:48028571-48028580
8	CTCF	chr7:48028540-48028690	WERI-Rb-1	eye:	n/a	chr7:48028571-48028580
9	CTCF	chr7:48028520-48028670	HPF	lung:	n/a	chr7:48028571-48028580
10	CTCF	chr7:48028520-48028670	HMF	breast:	n/a	chr7:48028571-48028580
11	CTCF	chr7:48028477-48028668	SK-N-SH_RA	brain:	n/a	chr7:48028571-48028580
12	CTCF	chr7:48028506-48028688	Fibrobl	skin:	n/a	chr7:48028571-48028580
13	CTCF	chr7:48028600-48028750	HFF-Myc	foreskin:	n/a	n/a
14	MAX	chr7:48028523-48028723	NB4	blood:	n/a	n/a
15	GATA3	chr7:48028436-48028852	SH-SY5Y	brain:	n/a	n/a
16	NR2F2	chr7:48028473-48028861	MCF-7	breast:	n/a	n/a
17	CTCF	chr7:48028520-48028670	HUVEC	blood vessel:	n/a	chr7:48028571-48028580
18	CTCF	chr7:48028520-48028670	GM06990	blood:	n/a	chr7:48028571-48028580
19	RAD21	chr7:48028420-48028720	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr7:48028560-48028710	WI-38	lung:	n/a	chr7:48028571-48028580
21	CTCF	chr7:48028418-48028868	MCF-7	breast:	n/a	chr7:48028571-48028580
22	GATA3	chr7:48028357-48028903	MCF-7	breast:	n/a	n/a
23	CTCF	chr7:48028540-48028690	BJ	skin:	n/a	chr7:48028571-48028580
24	SMC3	chr7:48028329-48028716	Hela-S3	cervix:	n/a	n/a
25	GATA2	chr7:48028413-48028721	SH-SY5Y	brain:	n/a	n/a
26	CTCF	chr7:48028520-48028670	AG04450	lung:	n/a	chr7:48028571-48028580
27	CTCF	chr7:48028533-48028672	A549	lung:	n/a	chr7:48028571-48028580
28	CTCF	chr7:48028389-48028754	IMR90	lung:	n/a	chr7:48028571-48028580
29	CTCF	chr7:48028475-48028701	Gliobla	brain:	n/a	chr7:48028571-48028580
30	RAD21	chr7:48028439-48028820	HCT-116	colon:	n/a	n/a
31	ZNF143	chr7:48028542-48028725	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr7:48028540-48028690	GM12865	blood:	n/a	chr7:48028571-48028580
33	CTCF	chr7:48028520-48028670	AG09319	gingival:	n/a	chr7:48028571-48028580
34	CTCF	chr7:48028473-48028680	HUVEC	blood vessel:	n/a	chr7:48028571-48028580
35	CTCF	chr7:48028481-48028700	GM12878	blood:	n/a	chr7:48028571-48028580
36	CTCF	chr7:48028520-48028670	GM12866	blood:	n/a	chr7:48028571-48028580
37	RAD21	chr7:48028428-48028723	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr7:48028470-48028665	K562	blood:	n/a	chr7:48028571-48028580
39	CTCF	chr7:48028540-48028690	HVMF	connective:	n/a	chr7:48028571-48028580
40	CTCF	chr7:48028540-48028690	NHLF	lung:	n/a	chr7:48028571-48028580
41	ARID3A	chr7:48028484-48028732	HepG2	liver:	n/a	n/a
42	CTCF	chr7:48028520-48028670	HEK293	kidney:	n/a	chr7:48028571-48028580
43	CTCF	chr7:48028540-48028690	HAc	cerebellar:	n/a	chr7:48028571-48028580
44	RAD21	chr7:48028455-48028752	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr7:48028437-48028692	SK-N-SH_RA	brain:	n/a	chr7:48028571-48028580
46	CTCF	chr7:48028520-48028670	HPAF	blood vessel:	n/a	chr7:48028571-48028580
47	RAD21	chr7:48028448-48028738	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr7:48028540-48028690	NHEK	skin:	n/a	chr7:48028571-48028580
49	CTCF	chr7:48028540-48028690	K562	blood:	n/a	chr7:48028571-48028580
50	CTCF	chr7:48028520-48028670	MCF-7	breast:	n/a	chr7:48028571-48028580

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:48028663-48028713	PFSK-1	brain:	n/a
2	chr7:48028663-48028713	HAEpiC	amniotic membrane:	n/a
3	chr7:48028663-48028713	HL-60	blood:	n/a
4	chr7:48028663-48028713	HRE	kidney:	n/a
5	chr7:48028663-48028713	ECC-1	luminal epithelium:	n/a
6	chr7:48028663-48028713	PrEC	prostate:	n/a
7	chr7:48028663-48028713	GM12892	blood:	n/a
8	chr7:48028663-48028713	HEEpiC	esophagus:	n/a
9	chr7:48028663-48028713	CMK	blood:	n/a
10	chr7:48028663-48028713	GM12891	blood:	n/a
11	chr7:48028663-48028713	T-47D	breast:	n/a
12	chr7:48028663-48028713	GM19239	blood:	n/a
13	chr7:48028663-48028713	SKMC	muscle:	n/a
14	chr7:48028663-48028713	GM06990	blood:	n/a
15	chr7:48028663-48028713	HIPEpiC	eye:	n/a
16	chr7:48028663-48028713	GM12878	blood:	n/a
17	chr7:48028663-48028713	ovcar-3	ovarian:	n/a
18	chr7:48028663-48028713	Jurkat	blood:	n/a
19	chr7:48028663-48028713	AG04450	lung:	fetal
20	chr7:48028663-48028713	BJ	skin:	n/a
21	chr7:48028663-48028713	HPAEpiC	pulmonary alveolar:	n/a
22	chr7:48028663-48028713	SK-N-MC	brain:	n/a
23	chr7:48028663-48028713	AoSMC	blood vessel:	n/a
24	chr7:48028663-48028713	IMR90	lung:	fetal
25	chr7:48028663-48028713	SAEC	small airway:	n/a
26	chr7:48028663-48028713	Caco-2	colon:	n/a
27	chr7:48028663-48028713	HRCEpiC	kidney:	n/a
28	chr7:48028663-48028713	NB4	blood:	n/a
29	chr7:48028663-48028713	A549	lung:	n/a
30	chr7:48028663-48028713	HUVEC	blood vessel:	n/a
31	chr7:48028663-48028713	BE2_C	brain:	n/a
32	chr7:48028663-48028713	SK-N-SH_RA	brain:	n/a
33	chr7:48028663-48028713	HepG2	liver:	n/a
34	chr7:48028663-48028713	Hepatocyte	liver:	n/a
35	chr7:48028663-48028713	HCPEpiC	choroid plexus:	n/a
36	chr7:48028663-48028713	HEK293	kidney:	embryo
37	chr7:48028663-48028713	PANC-1	pancreas:	n/a
38	chr7:48028663-48028713	MCF10A-Er-Src	breast:	n/a
39	chr7:48028663-48028713	NH-A	brain:	n/a
40	chr7:48028663-48028713	U87	brain:	n/a
41	chr7:48028663-48028713	Hela-S3	cervix:	n/a
42	chr7:48028663-48028713	HCF	heart:	n/a
43	chr7:48028663-48028713	MCF-7	breast:	n/a
44	chr7:48028663-48028713	NHBE	bronchial:	n/a
45	chr7:48028663-48028713	LNCaP	prostate:	n/a
46	chr7:48028663-48028713	HCM	heart:	n/a
47	chr7:48028663-48028713	HRPEpiC	eye:	n/a
48	chr7:48028663-48028713	AG04449	skin:	fetal
49	chr7:48028663-48028713	NHDF-neo	bronchial:	n/a
50	chr7:48028663-48028713	HMEC	breast:	n/a

Variant related genes	Relation type
SUN3	TF binding region
SUN3	CpG island

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17131957	1.00[AMR][1000 genomes]
rs2307253	1.00[AMR][1000 genomes]
rs3176484	1.00[AMR][1000 genomes]
rs3176552	1.00[AMR][1000 genomes]
rs3176603	1.00[AMR][1000 genomes]
rs3176608	1.00[AMR][1000 genomes]
rs3176621	1.00[AMR][1000 genomes]
rs59522165	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48019400-48028800	Weak transcription	Fetal Lung	lung
2	chr7:48019800-48031600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:48023200-48031200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:48024200-48030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:48027600-48029400	Weak transcription	Placenta	Placenta
6	chr7:48028200-48029000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr7:48028200-48029600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:48028400-48031200	Enhancers	HepG2	liver
9	chr7:48028600-48028800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:48028600-48029000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:48028600-48029000	Enhancers	A549	lung
12	chr7:48028600-48029400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr7:48028600-48029800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:48028600-48029800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr7:48028600-48030000	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links