Variant report

Variant	rs3735460
Chromosome Location	chr7:7679885-7679886
allele	C/T
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	POLR2A	chr7:7679078-7681429	HepG2	liver:	n/a	n/a
2	POU2F2	chr7:7679701-7680956	GM12878	blood:	n/a	chr7:7679901-7679913
3	CHD2	chr7:7679821-7681280	K562	blood:	n/a	n/a
4	POLR2A	chr7:7679589-7680817	PFSK-1	brain:	n/a	n/a
5	EGR1	chr7:7679793-7681078	HCT-116	colon:	n/a	chr7:7680614-7680628 chr7:7680616-7680626 chr7:7680615-7680626 chr7:7679837-7679850 chr7:7680311-7680324 chr7:7680615-7680626 chr7:7680243-7680252 chr7:7680616-7680626
6	HDAC2	chr7:7679834-7680305	HepG2	liver:	n/a	n/a
7	SIN3AK20	chr7:7679772-7680872	A549	lung:	n/a	n/a
8	MAX	chr7:7679672-7680703	HepG2	liver:	n/a	n/a
9	CEBPB	chr7:7679844-7680702	K562	blood:	n/a	n/a
10	GABPA	chr7:7679474-7681187	MCF-7	breast:	n/a	chr7:7680866-7680880
11	CHD2	chr7:7679573-7681141	Hela-S3	cervix:	n/a	n/a
12	ATF2	chr7:7679724-7680648	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr7:7679818-7680916	K562	blood:	n/a	n/a
14	YY1	chr7:7679755-7680723	ECC-1	luminal epithelium:	n/a	n/a
15	YY1	chr7:7679696-7680734	GM12892	blood:	n/a	n/a
16	E2F4	chr7:7679659-7681013	Hela-S3	cervix:	n/a	chr7:7679772-7679783 chr7:7679769-7679786 chr7:7679776-7679783 chr7:7679769-7679786 chr7:7680071-7680082 chr7:7680622-7680631
17	SMARCC1	chr7:7679092-7681404	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr7:7679855-7680692	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr7:7678812-7681214	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr7:7679266-7681091	GM18951	blood:	n/a	n/a
21	MAFK	chr7:7679337-7681481	Hela-S3	cervix:	n/a	chr7:7679735-7679746 chr7:7681124-7681133 chr7:7681140-7681155 chr7:7679683-7679700 chr7:7681123-7681133
22	SMC3	chr7:7679749-7679949	K562	blood:	n/a	n/a
23	TAF1	chr7:7679437-7680760	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr7:7679081-7680950	PANC-1	pancreas:	n/a	n/a
25	PBX3	chr7:7679789-7680752	A549	lung:	n/a	n/a
26	HEY1	chr7:7679745-7681126	HepG2	liver:	n/a	n/a
27	YY1	chr7:7679811-7680270	A549	lung:	n/a	n/a
28	POLR2A	chr7:7679333-7680707	HUVEC	blood vessel:	n/a	n/a
29	ELK1	chr7:7679879-7680622	K562	blood:	n/a	chr7:7680243-7680252 chr7:7680243-7680252
30	POLR2A	chr7:7679827-7680177	HepG2	liver:	n/a	n/a
31	MAX	chr7:7679392-7681227	MCF-7	breast:	n/a	n/a
32	MYC	chr7:7679205-7680982	NB4	blood:	n/a	n/a
33	POLR2A	chr7:7679481-7681387	K562	blood:	n/a	n/a
34	POLR2A	chr7:7679451-7681228	HepG2	liver:	n/a	n/a
35	REST	chr7:7679879-7680229	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr7:7679505-7680748	HCT-116	colon:	n/a	n/a
37	ETS1	chr7:7679731-7680729	GM12878	blood:	n/a	chr7:7680244-7680254 chr7:7680243-7680252 chr7:7680282-7680293 chr7:7680243-7680252 chr7:7680283-7680293 chr7:7680282-7680291
38	EP300	chr7:7679492-7681010	GM12878	blood:	n/a	chr7:7680283-7680290 chr7:7680244-7680251
39	HEY1	chr7:7679381-7681123	K562	blood:	n/a	n/a
40	GATA3	chr7:7679759-7680957	A549	lung:	n/a	n/a
41	ZNF143	chr7:7679503-7680861	GM12878	blood:	n/a	n/a
42	YY1	chr7:7679816-7680506	HCT-116	colon:	n/a	n/a
43	TAF1	chr7:7679858-7680195	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr7:7679144-7681438	Hela-S3	cervix:	n/a	n/a
45	NR2F2	chr7:7679862-7681224	K562	blood:	n/a	n/a
46	IRF4	chr7:7679780-7680758	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr7:7679809-7680763	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr7:7679157-7680899	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr7:7679769-7680945	GM18526	blood:	n/a	n/a
50	TAF1	chr7:7679737-7680864	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:41466087..41467053-chr7:7679547..7680423,2	Hela-S3	cervix:
2	chr7:7602591..7604094-chr7:7678775..7680350,2	K562	blood:
3	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:
4	chr17:62502252..62503126-chr7:7679849..7680803,2	Hela-S3	cervix:
5	chr7:7679018..7681584-chr7:8008760..8011156,4	K562	blood:
6	chr15:41165970..41166558-chr7:7679740..7680262,2	Hela-S3	cervix:
7	chr7:7673907..7678610-chr7:7678691..7681851,6	MCF-7	breast:
8	chr7:7605040..7608458-chr7:7677009..7681661,8	K562	blood:
9	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
10	chr7:7672448..7678421-chr7:7678475..7681557,8	K562	blood:
11	chr6:24720585..24722124-chr7:7679223..7680620,4	Hela-S3	cervix:
12	chr7:7678479..7681346-chr7:8300009..8302111,2	K562	blood:
13	chr11:64018519..64019489-chr7:7679437..7680045,2	Hela-S3	cervix:
14	chr17:74732854..74733643-chr7:7679556..7680144,2	NB4	blood:

Variant related genes	Relation type
RPA3	TF binding region
RPA3-AS1	TF binding region
ENSG00000108654	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000161547	Chromatin interaction
ENSG00000233108	Chromatin interaction
ENSG00000003147	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000106415	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000244239	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000149782	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000092931	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2301936	0.80[EUR][1000 genomes]
rs28915995	1.00[ASW][hapmap]
rs6463710	0.89[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3735460	RPA3	cis	lesional skin	skin_eQTL
rs3735460	ENSG00000106399	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7678600-7681200	Active TSS	HMEC	breast
2	chr7:7678800-7681200	Active TSS	A549	lung
3	chr7:7678800-7681400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr7:7678800-7681400	Active TSS	K562	blood
5	chr7:7678800-7681600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:7679000-7680000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr7:7679000-7680400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr7:7679000-7680800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr7:7679000-7681000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:7679000-7681000	Active TSS	Brain Anterior Caudate	brain
11	chr7:7679000-7681000	Active TSS	Fetal Kidney	kidney
12	chr7:7679000-7681000	Active TSS	NH-A	brain
13	chr7:7679000-7681200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:7679000-7681200	Active TSS	Brain Angular Gyrus	brain
15	chr7:7679000-7681200	Active TSS	Fetal Muscle Trunk	muscle
16	chr7:7679000-7681200	Active TSS	Psoas Muscle	Psoas
17	chr7:7679000-7681200	Active TSS	GM12878-XiMat	blood
18	chr7:7679000-7681400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr7:7679000-7681400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:7679000-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:7679000-7681400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr7:7679000-7681400	Active TSS	NHLF	lung
23	chr7:7679000-7681600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr7:7679000-7681600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:7679000-7681600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:7679000-7681800	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr7:7679000-7682000	Active TSS	Fetal Intestine Small	intestine
30	chr7:7679200-7680000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr7:7679200-7680000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr7:7679200-7681000	Active TSS	Colon Smooth Muscle	Colon
33	chr7:7679200-7681000	Active TSS	Fetal Intestine Large	intestine
34	chr7:7679200-7681000	Active TSS	HSMM	muscle
35	chr7:7679200-7681200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:7679200-7681200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:7679200-7681200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr7:7679200-7681200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:7679200-7681200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:7679200-7681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:7679200-7681200	Active TSS	Lung	lung
42	chr7:7679200-7681200	Active TSS	NHDF-Ad	bronchial
43	chr7:7679200-7681400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:7679200-7681400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr7:7679200-7681400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:7679200-7681400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:7679200-7681400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:7679200-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:7679200-7681400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:7679200-7681400	Active TSS	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links