Variant report

Variant	rs2531174
Chromosome Location	chr4:15940205-15940206
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	SMC3	chr4:15939735-15940221	Hela-S3	cervix:	n/a	chr4:15939769-15939779
2	MAX	chr4:15939635-15940382	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr4:15939565-15940334	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr4:15940160-15940310	SAEC	small airway:	n/a	n/a
5	PRDM1	chr4:15939918-15940282	Hela-S3	cervix:	n/a	chr4:15940080-15940095 chr4:15940085-15940094
6	NFIC	chr4:15939701-15940436	ECC-1	luminal epithelium:	n/a	n/a
7	MYC	chr4:15939798-15940218	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:15939712-15940305	ECC-1	luminal epithelium:	n/a	n/a
9	SP1	chr4:15939763-15940429	HCT-116	colon:	n/a	chr4:15940054-15940064 chr4:15940054-15940064
10	MYC	chr4:15939855-15940209	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr4:15939569-15940619	ECC-1	luminal epithelium:	n/a	chr4:15940557-15940571
12	STAT3	chr4:15939966-15940245	MCF10A-Er-Src	breast:	n/a	chr4:15940080-15940091
13	POLR2A	chr4:15934291-15944634	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr4:15940060-15940210	HEEpiC	esophagus:	n/a	n/a
15	TCF12	chr4:15939531-15940459	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr4:15940140-15940290	HMEC	breast:	n/a	n/a
17	MAX	chr4:15939699-15940347	ECC-1	luminal epithelium:	n/a	n/a
18	NFIC	chr4:15939667-15940481	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr4:15939620-15940348	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr4:15939610-15940442	HCT-116	colon:	n/a	n/a
21	POLR2A	chr4:15939052-15940305	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FGFBP1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2072313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246196	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531138	0.80[ASN][1000 genomes]
rs2531141	0.98[ASN][1000 genomes]
rs2531143	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2532063	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2532064	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv878715	chr4:15840839-15947493	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv878716	chr4:15911031-15947493	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv878717	chr4:15920423-15950731	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv593769	chr4:15921471-15943140	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv878718	chr4:15925170-15947493	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a
8	nsv878719	chr4:15930961-15947493	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a
9	esv3357658	chr4:15940054-15944352	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15938200-15941600	Weak transcription	Right Atrium	heart
2	chr4:15939200-15940400	Enhancers	Stomach Mucosa	stomach
3	chr4:15939600-15940400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:15939600-15940400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:15939600-15940400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:15939600-15940600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:15939800-15940400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:15939800-15940400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:15939800-15940400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:15939800-15941000	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr4:15939800-15941000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr4:15940000-15940400	Enhancers	Colonic Mucosa	Colon
13	chr4:15940000-15940400	Enhancers	Fetal Intestine Large	intestine
14	chr4:15940000-15940400	Flanking Active TSS	HMEC	breast
15	chr4:15940000-15940600	Enhancers	Hela-S3	cervix
16	chr4:15940000-15940800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:15940000-15941000	Flanking Active TSS	NHEK	skin
18	chr4:15940000-15950600	Weak transcription	Esophagus	oesophagus
19	chr4:15940200-15940400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:15940200-15940400	Enhancers	Thymus	Thymus
21	chr4:15940200-15940400	Enhancers	A549	lung
22	chr4:15940200-15940600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:15940200-15941000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr4:15940200-15983600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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