Variant report

Variant	rs2886927
Chromosome Location	chr4:74730231-74730232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:165)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:165 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:74730091-74730495	GM12878	blood:	n/a	n/a
2	CTCF	chr4:74730200-74730350	GM06990	blood:	n/a	n/a
3	CTCF	chr4:74730167-74730402	GM12878	blood:	n/a	n/a
4	CTCF	chr4:74730200-74730350	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr4:74730180-74730330	GM12801	blood:	n/a	n/a
6	CTCF	chr4:74730163-74730354	T-47D	breast:	n/a	n/a
7	RAD21	chr4:74730008-74730550	ECC-1	luminal epithelium:	n/a	n/a
8	RAD21	chr4:74730111-74730489	SK-N-SH_RA	brain:	n/a	n/a
9	ZNF143	chr4:74730092-74730430	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr4:74730220-74730370	HepG2	liver:	n/a	n/a
11	USF2	chr4:74730103-74730327	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr4:74730200-74730350	HL-60	blood:	n/a	n/a
13	CTCF	chr4:74730220-74730370	HEEpiC	esophagus:	n/a	n/a
14	EP300	chr4:74730137-74730359	K562	blood:	n/a	n/a
15	CTCF	chr4:74730119-74730370	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr4:74730163-74730395	GM19239	blood:	n/a	n/a
17	RAD21	chr4:74729989-74730565	HCT-116	colon:	n/a	n/a
18	CTCF	chr4:74730206-74730367	Medullo	brain:	n/a	n/a
19	RAD21	chr4:74730094-74730515	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr4:74730220-74730370	GM12870	blood:	n/a	n/a
21	CTCF	chr4:74730200-74730350	HFF-Myc	foreskin:	n/a	n/a
22	RAD21	chr4:74730159-74730415	MCF-7	breast:	n/a	n/a
23	CTCF	chr4:74730220-74730370	BJ	skin:	n/a	n/a
24	CTCF	chr4:74730000-74730658	A549	lung:	n/a	n/a
25	CTCF	chr4:74730220-74730370	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr4:74730062-74730461	K562	blood:	n/a	n/a
27	RAD21	chr4:74730046-74730431	A549	lung:	n/a	n/a
28	WRNIP1	chr4:74730054-74730349	GM12878	blood:	n/a	n/a
29	SMC3	chr4:74730107-74730477	K562	blood:	n/a	n/a
30	CTCF	chr4:74730200-74730350	AG04450	lung:	n/a	n/a
31	CTCF	chr4:74730220-74730370	HBMEC	blood vessel:	n/a	n/a
32	CTCF	chr4:74730160-74730310	AG09309	skin:	n/a	n/a
33	RAD21	chr4:74730000-74730431	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr4:74730040-74730535	A549	lung:	n/a	n/a
35	CTCF	chr4:74730189-74730385	GM10266	blood:	n/a	n/a
36	CTCF	chr4:74730095-74730425	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr4:74730220-74730370	GM12864	blood:	n/a	n/a
38	CTCF	chr4:74730200-74730350	GM12875	blood:	n/a	n/a
39	RAD21	chr4:74730086-74730402	SK-N-SH_RA	brain:	n/a	n/a
40	SMC3	chr4:74730153-74730435	HepG2	liver:	n/a	n/a
41	MAFK	chr4:74730199-74730397	K562	blood:	n/a	n/a
42	CTCF	chr4:74730220-74730370	GM12869	blood:	n/a	n/a
43	CTCF	chr4:74730180-74730330	AG04450	lung:	n/a	n/a
44	CTCF	chr4:74730220-74730370	Caco-2	colon:	n/a	n/a
45	RAD21	chr4:74730138-74730419	A549	lung:	n/a	n/a
46	CTCF	chr4:74730200-74730350	HRPEpiC	eye:	n/a	n/a
47	ZNF143	chr4:74730114-74730345	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr4:74730182-74730385	A549	lung:	n/a	n/a
49	CTCF	chr4:74730089-74730377	K562	blood:	n/a	n/a
50	RAD21	chr4:74730008-74730481	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:74528090..74529212-chr4:74729841..74730672,4	MCF-7	breast:
2	chr4:74528297..74529106-chr4:74730060..74730707,3	K562	blood:
3	chr4:74528321..74529495-chr4:74729762..74730750,4	MCF-7	breast:
4	chr4:74718960..74724397-chr4:74728393..74732828,5	K562	blood:
5	chr4:74719674..74726110-chr4:74728599..74734688,9	K562	blood:
6	chr4:74724927..74730400-chr4:74731637..74736149,6	K562	blood:

No data

Variant related genes	Relation type
CXCL1	TF binding region
ENSG00000163739	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16850137	0.91[JPT][hapmap]
rs2115691	0.87[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2367291	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];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097411	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs3097412	0.81[ASW][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap]
rs3111692	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3111694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117604	0.90[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4074	0.87[JPT][hapmap]
rs516224	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs58557052	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6858086	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs9991272	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2886927	THAP6	cis	parietal	SCAN
rs2886927	G3BP2	cis	parietal	SCAN
rs2886927	SEPT11	cis	parietal	SCAN
rs2886927	CXCL6	cis	parietal	SCAN
rs2886927	PF4V1	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74719400-74733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:74724200-74730600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:74726000-74734200	Weak transcription	HSMM	muscle
4	chr4:74726200-74733600	Weak transcription	NHDF-Ad	bronchial
5	chr4:74726400-74733800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:74728600-74734200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:74728800-74734000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:74729200-74733600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr4:74730000-74730400	Enhancers	NHEK	skin
10	chr4:74730000-74730600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:74730000-74730800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:74730000-74731800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:74730000-74732600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:74730200-74732000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links