Variant report

Variant	rs28898573
Chromosome Location	chr2:234597162-234597163
allele	A/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	USF1	chr2:234597082-234597252	HepG2	liver:	n/a	chr2:234597182-234597193
2	FOXA1	chr2:234597037-234597376	HepG2	liver:	n/a	n/a
3	FOXA2	chr2:234597052-234597363	HepG2	liver:	n/a	n/a
4	MAX	chr2:234597031-234597271	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXA2	chr2:234597024-234597405	A549	lung:	n/a	n/a
6	FOXA1	chr2:234597072-234597409	HepG2	liver:	n/a	n/a
7	TCF12	chr2:234596802-234597555	A549	lung:	n/a	chr2:234597305-234597312
8	FOXA1	chr2:234597047-234597404	HepG2	liver:	n/a	n/a
9	EP300	chr2:234597023-234597315	HepG2	liver:	n/a	n/a
10	FOXA1	chr2:234596953-234597498	HepG2	liver:	n/a	n/a
11	KAP1	chr2:234596969-234597265	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
2	chr2:234593709..234597691-chr2:234598690..234601824,5	MCF-7	breast:
3	chr2:234590573..234592991-chr2:234596085..234597690,2	MCF-7	breast:

Variant related genes	Relation type
UGT1A6	TF binding region
ENSG00000244122	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10182818	1.00[EUR][1000 genomes]
rs13389374	1.00[EUR][1000 genomes]
rs13390054	1.00[EUR][1000 genomes]
rs13395852	1.00[EUR][1000 genomes]
rs13398912	1.00[EUR][1000 genomes]
rs13401703	1.00[EUR][1000 genomes]
rs13403667	1.00[EUR][1000 genomes]
rs13406202	1.00[EUR][1000 genomes]
rs28898571	1.00[EUR][1000 genomes]
rs28898598	1.00[EUR][1000 genomes]
rs28899474	1.00[EUR][1000 genomes]
rs28899479	1.00[EUR][1000 genomes]
rs28900378	1.00[EUR][1000 genomes]
rs28900380	1.00[EUR][1000 genomes]
rs28900396	1.00[EUR][1000 genomes]
rs28968515	1.00[EUR][1000 genomes]
rs28969703	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28969712	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28969974	1.00[EUR][1000 genomes]
rs28970005	1.00[EUR][1000 genomes]
rs28970006	1.00[EUR][1000 genomes]
rs28970014	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28970015	1.00[EUR][1000 genomes]
rs34652311	1.00[EUR][1000 genomes]
rs45498701	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45505392	1.00[EUR][1000 genomes]
rs45548336	1.00[EUR][1000 genomes]
rs45568235	1.00[EUR][1000 genomes]
rs73121108	1.00[EUR][1000 genomes]
rs73123128	1.00[EUR][1000 genomes]
rs73123133	1.00[EUR][1000 genomes]
rs73123137	1.00[EUR][1000 genomes]
rs73123148	1.00[EUR][1000 genomes]
rs73123150	1.00[EUR][1000 genomes]
rs9287602	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
5	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234590000-234597800	Weak transcription	Colonic Mucosa	Colon
2	chr2:234590800-234597400	Weak transcription	Liver	Liver
3	chr2:234590800-234599800	Weak transcription	Esophagus	oesophagus
4	chr2:234592400-234597200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:234593200-234598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:234594400-234597600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:234595800-234597400	Weak transcription	Hela-S3	cervix
8	chr2:234596800-234600600	Enhancers	Stomach Mucosa	stomach
9	chr2:234597000-234597200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:234597000-234597600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr2:234597000-234597800	Enhancers	Gastric	stomach
12	chr2:234597000-234598400	Enhancers	Primary hematopoietic stem cells	blood
13	chr2:234597000-234598400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:234597000-234598600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:234597000-234599000	Enhancers	A549	lung
16	chr2:234597000-234600400	Enhancers	Sigmoid Colon	Sigmoid Colon

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