Variant report

Variant	rs3735461
Chromosome Location	chr7:7679644-7679645
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	POLR2A	chr7:7679589-7680817	PFSK-1	brain:	n/a	n/a
3	PAX5	chr7:7679375-7679769	GM12878	blood:	n/a	n/a
4	IRF3	chr7:7679568-7679757	GM12878	blood:	n/a	n/a
5	GABPA	chr7:7679474-7681187	MCF-7	breast:	n/a	chr7:7680866-7680880
6	CHD2	chr7:7679573-7681141	Hela-S3	cervix:	n/a	n/a
7	SMARCC1	chr7:7679092-7681404	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:7678812-7681214	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr7:7679266-7681091	GM18951	blood:	n/a	n/a
10	MAFK	chr7:7679337-7681481	Hela-S3	cervix:	n/a	chr7:7679735-7679746 chr7:7681124-7681133 chr7:7681140-7681155 chr7:7679683-7679700 chr7:7681123-7681133
11	TAF1	chr7:7679437-7680760	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr7:7679081-7680950	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr7:7679333-7680707	HUVEC	blood vessel:	n/a	n/a
14	MAX	chr7:7679392-7681227	MCF-7	breast:	n/a	n/a
15	MYC	chr7:7679205-7680982	NB4	blood:	n/a	n/a
16	POLR2A	chr7:7679481-7681387	K562	blood:	n/a	n/a
17	POLR2A	chr7:7679451-7681228	HepG2	liver:	n/a	n/a
18	POLR2A	chr7:7679505-7680748	HCT-116	colon:	n/a	n/a
19	EP300	chr7:7679492-7681010	GM12878	blood:	n/a	chr7:7680283-7680290 chr7:7680244-7680251
20	HEY1	chr7:7679381-7681123	K562	blood:	n/a	n/a
21	ZNF143	chr7:7679503-7680861	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:7679144-7681438	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr7:7679157-7680899	PANC-1	pancreas:	n/a	n/a
24	TCF12	chr7:7679592-7681097	ECC-1	luminal epithelium:	n/a	n/a
25	MAFF	chr7:7679485-7680067	K562	blood:	n/a	n/a
26	POLR2A	chr7:7679344-7681083	GM12891	blood:	n/a	n/a
27	POLR2A	chr7:7679060-7681323	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:7679471-7681088	K562	blood:	n/a	n/a
29	BHLHE40	chr7:7679570-7681170	GM12878	blood:	n/a	n/a
30	RCOR1	chr7:7679512-7680981	GM12878	blood:	n/a	n/a
31	MAX	chr7:7679352-7681008	ECC-1	luminal epithelium:	n/a	n/a
32	YY1	chr7:7679639-7680293	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr7:7678754-7682381	SK-N-SH	brain:	n/a	n/a
34	CEBPB	chr7:7679546-7680759	Hela-S3	cervix:	n/a	n/a
35	SIN3AK20	chr7:7679531-7681354	MCF-7	breast:	n/a	n/a
36	YY1	chr7:7679415-7681039	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:7678993-7681329	GM12892	blood:	n/a	n/a
38	MAFK	chr7:7679518-7681304	HepG2	liver:	n/a	chr7:7679735-7679746 chr7:7681124-7681133 chr7:7681140-7681155 chr7:7679683-7679700 chr7:7681123-7681133
39	POLR2A	chr7:7679463-7680953	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr7:7679567-7680933	H1-hESC	embryonic stem cell:	n/a	n/a
41	FOXM1	chr7:7679403-7681227	GM12878	blood:	n/a	n/a
42	POLR2A	chr7:7679463-7680797	GM10847	blood:	n/a	n/a
43	FOXM1	chr7:7679637-7680646	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr7:7679110-7681220	GM12891	blood:	n/a	n/a
45	POLR2A	chr7:7679078-7681236	GM19099	blood:	n/a	n/a
46	ELK1	chr7:7679500-7680793	GM12878	blood:	n/a	chr7:7680243-7680252 chr7:7680243-7680252
47	HDAC2	chr7:7679480-7680981	MCF-7	breast:	n/a	n/a
48	GABPA	chr7:7679644-7680929	SK-N-SH	brain:	n/a	chr7:7680866-7680880
49	TCF12	chr7:7679507-7680935	A549	lung:	n/a	n/a
50	MAX	chr7:7679479-7681139	GM12878	blood:	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	chr7:7679018..7681584-chr7:8008760..8011156,4	K562	blood:
5	chr7:7673907..7678610-chr7:7678691..7681851,6	MCF-7	breast:
6	chr7:7605040..7608458-chr7:7677009..7681661,8	K562	blood:
7	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
8	chr7:7672448..7678421-chr7:7678475..7681557,8	K562	blood:
9	chr6:24720585..24722124-chr7:7679223..7680620,4	Hela-S3	cervix:
10	chr7:7678479..7681346-chr7:8300009..8302111,2	K562	blood:
11	chr11:64018519..64019489-chr7:7679437..7680045,2	Hela-S3	cervix:
12	chr17:74732854..74733643-chr7:7679556..7680144,2	NB4	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10258834	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10280932	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11773681	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12539359	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13229270	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4397305	0.83[ASN][1000 genomes]
rs6962587	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs3735461	COL28A1	cis	parietal	SCAN
rs3735461	COL28A1	cis	cerebellum	SCAN

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	chr7:7679000-7679800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr7:7679000-7680000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr7:7679000-7680400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr7:7679000-7680800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr7:7679000-7681000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:7679000-7681000	Active TSS	Brain Anterior Caudate	brain
12	chr7:7679000-7681000	Active TSS	Fetal Kidney	kidney
13	chr7:7679000-7681000	Active TSS	NH-A	brain
14	chr7:7679000-7681200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:7679000-7681200	Active TSS	Brain Angular Gyrus	brain
16	chr7:7679000-7681200	Active TSS	Fetal Muscle Trunk	muscle
17	chr7:7679000-7681200	Active TSS	Psoas Muscle	Psoas
18	chr7:7679000-7681200	Active TSS	GM12878-XiMat	blood
19	chr7:7679000-7681400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr7:7679000-7681400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr7:7679000-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:7679000-7681400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr7:7679000-7681400	Active TSS	NHLF	lung
24	chr7:7679000-7681600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr7:7679000-7681600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:7679000-7681600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:7679000-7681600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:7679000-7681800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:7679000-7682000	Active TSS	Fetal Intestine Small	intestine
31	chr7:7679200-7679800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr7:7679200-7680000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr7:7679200-7680000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr7:7679200-7681000	Active TSS	Colon Smooth Muscle	Colon
35	chr7:7679200-7681000	Active TSS	Fetal Intestine Large	intestine
36	chr7:7679200-7681000	Active TSS	HSMM	muscle
37	chr7:7679200-7681200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr7:7679200-7681200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:7679200-7681200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr7:7679200-7681200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:7679200-7681200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr7:7679200-7681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:7679200-7681200	Active TSS	Lung	lung
44	chr7:7679200-7681200	Active TSS	NHDF-Ad	bronchial
45	chr7:7679200-7681400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:7679200-7681400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr7:7679200-7681400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr7:7679200-7681400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:7679200-7681400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:7679200-7681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links