Variant report

Variant	rs4298142
Chromosome Location	chr4:110725748-110725749
allele	C/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	SMC3	chr4:110725030-110725790	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr4:110725140-110725791	HCT-116	colon:	n/a	n/a
3	SMC3	chr4:110725078-110725772	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr4:110725215-110725792	MCF-7	breast:	n/a	chr4:110725568-110725576
5	GATA3	chr4:110725197-110725794	MCF-7	breast:	n/a	chr4:110725568-110725576
6	RAD21	chr4:110725204-110725769	ECC-1	luminal epithelium:	n/a	n/a
7	RAD21	chr4:110725114-110725828	HCT-116	colon:	n/a	n/a
8	GATA3	chr4:110725193-110725805	SK-N-SH	brain:	n/a	chr4:110725568-110725576
9	GATA2	chr4:110725170-110725780	SH-SY5Y	brain:	n/a	n/a
10	GATA3	chr4:110725201-110725845	SK-N-SH	brain:	n/a	chr4:110725568-110725576
11	GATA2	chr4:110725337-110725767	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr4:110725078-110725812	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr4:110725056-110725890	SK-N-SH	brain:	n/a	n/a
14	GATA1	chr4:110725342-110725779	PBDE	blood:	n/a	n/a
15	RAD21	chr4:110725261-110725786	MCF-7	breast:	n/a	n/a
16	GATA3	chr4:110725373-110725791	T-47D	breast:	n/a	chr4:110725568-110725576
17	GATA3	chr4:110725292-110725775	T-47D	breast:	n/a	chr4:110725568-110725576
18	RAD21	chr4:110725091-110725807	HCT-116	colon:	n/a	n/a
19	RAD21	chr4:110725186-110725790	A549	lung:	n/a	n/a
20	CTCF	chr4:110725191-110725806	A549	lung:	n/a	n/a
21	RAD21	chr4:110725273-110725754	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110725244..110727161-chr4:110727468..110730412,2	MCF-7	breast:
2	chr4:110623744..110624336-chr4:110725064..110725952,2	MCF-7	breast:
3	chr4:110724812..110728911-chr4:110730126..110732446,4	K562	blood:
4	chr4:110705166..110707910-chr4:110724039..110725781,2	K562	blood:
5	chr4:110597890..110598667-chr4:110725301..110725981,3	MCF-7	breast:
6	chr4:110621205..110625752-chr4:110723387..110726377,6	MCF-7	breast:

Variant related genes	Relation type
CFI	TF binding region
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10000072	0.89[ASN][1000 genomes]
rs10000458	0.89[ASN][1000 genomes]
rs10004794	0.89[ASN][1000 genomes]
rs10011911	0.88[ASN][1000 genomes]
rs10024583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029485	0.85[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs1002989	0.83[ASW][hapmap];0.81[MKK][hapmap]
rs10049642	0.88[ASN][1000 genomes]
rs10434000	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461144	0.89[ASN][1000 genomes]
rs11932501	0.89[ASN][1000 genomes]
rs11932539	0.89[ASN][1000 genomes]
rs11932552	0.89[ASN][1000 genomes]
rs11937379	0.89[ASN][1000 genomes]
rs17040841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28762207	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28785634	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28786383	0.89[ASN][1000 genomes]
rs28787106	0.89[ASN][1000 genomes]
rs28827596	0.89[ASN][1000 genomes]
rs28829108	0.89[ASN][1000 genomes]
rs28862613	0.89[ASN][1000 genomes]
rs28879996	0.89[ASN][1000 genomes]
rs4299582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333185	0.83[ASW][hapmap];0.81[MKK][hapmap]
rs4698785	0.89[ASN][1000 genomes]
rs4698786	0.89[ASN][1000 genomes]
rs4698787	0.89[ASN][1000 genomes]
rs4698788	0.85[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs4698790	0.81[CHB][hapmap]
rs884711	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994162	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110722600-110736200	Weak transcription	Pancreas	Pancrea
2	chr4:110722800-110735800	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:110723800-110727200	Enhancers	HepG2	liver
4	chr4:110724000-110725800	Enhancers	Liver	Liver
5	chr4:110724400-110735800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:110725400-110725800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:110725600-110725800	Enhancers	Fetal Intestine Large	intestine
8	chr4:110725600-110725800	Enhancers	Fetal Intestine Small	intestine
9	chr4:110725600-110725800	Enhancers	K562	blood

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