Variant report

Variant	rs28898590
Chromosome Location	chr2:234619422-234619423
allele	G/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	TCF12	chr2:234618903-234620639	A549	lung:	n/a	chr2:234620027-234620034
2	EP300	chr2:234618806-234619573	A549	lung:	n/a	n/a
3	CTCF	chr2:234618797-234620924	A549	lung:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
4	SP1	chr2:234618963-234619549	A549	lung:	n/a	n/a
5	EP300	chr2:234618830-234619527	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234474046..234476375-chr2:234618981..234621894,3	MCF-7	breast:
2	chr2:234400105..234405009-chr2:234616033..234619892,4	MCF-7	breast:
3	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
4	chr2:234613252..234614909-chr2:234617932..234620320,3	MCF-7	breast:
5	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
6	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
7	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
8	chr2:234388450..234390817-chr2:234616855..234619470,2	MCF-7	breast:
9	chr2:234366581..234368147-chr2:234619420..234621425,2	MCF-7	breast:

Variant related genes	Relation type
UGT1A8	TF binding region
ENSG00000224814	TF binding region
UGT1A5	TF binding region
ENSG00000077044	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11568318	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1551286	0.84[EUR][1000 genomes]
rs17862835	0.84[EUR][1000 genomes]
rs17862844	0.84[EUR][1000 genomes]
rs17862846	0.84[EUR][1000 genomes]
rs17862848	0.84[EUR][1000 genomes]
rs17862851	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862854	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862859	0.87[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17862874	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863784	0.87[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17863795	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863800	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17864666	0.84[EUR][1000 genomes]
rs17864670	0.84[EUR][1000 genomes]
rs17864671	0.84[EUR][1000 genomes]
rs17864675	0.84[EUR][1000 genomes]
rs17864689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868298	0.84[EUR][1000 genomes]
rs17868299	0.84[EUR][1000 genomes]
rs17868301	0.84[EUR][1000 genomes]
rs17868318	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17868320	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868338	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17868341	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17874945	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs34916116	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45507691	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56125405	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56143032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714486	0.95[EUR][1000 genomes]
rs6755571	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563478	0.84[EUR][1000 genomes]
rs7585521	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv963781	chr2:234618109-234626863	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv876017	chr2:234618243-234626972	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234615000-234619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:234615400-234620400	Weak transcription	Pancreas	Pancrea
3	chr2:234615600-234620000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:234617000-234619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:234617400-234619800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:234617400-234619800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:234617400-234620000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:234617800-234620400	Weak transcription	Esophagus	oesophagus
9	chr2:234617800-234631600	Weak transcription	Gastric	stomach
10	chr2:234618600-234621400	Enhancers	Liver	Liver
11	chr2:234618800-234620400	Enhancers	Hela-S3	cervix
12	chr2:234619200-234619600	Weak transcription	Stomach Mucosa	stomach
13	chr2:234619200-234619600	Weak transcription	NHEK	skin
14	chr2:234619400-234619800	Enhancers	A549	lung

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