Variant report

Variant	rs12998233
Chromosome Location	chr2:10160358-10160359
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	chr2:10160211-10160493	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr2:10160136-10160421	K562	blood:	n/a	n/a
3	CTCF	chr2:10160263-10160425	K562	blood:	n/a	n/a
4	CTCF	chr2:10160280-10160420	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr2:10160221-10160471	K562	blood:	n/a	n/a
6	MYC	chr2:10159803-10160385	K562	blood:	n/a	chr2:10160315-10160326 chr2:10160314-10160329 chr2:10159974-10159981 chr2:10160314-10160327 chr2:10160315-10160324 chr2:10160316-10160326 chr2:10160315-10160326 chr2:10160316-10160326 chr2:10160315-10160325 chr2:10160316-10160325
7	RAD21	chr2:10160165-10160532	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr2:10160149-10160414	K562	blood:	n/a	n/a
9	RAD21	chr2:10160094-10160574	H1-hESC	embryonic stem cell:	n/a	chr2:10160107-10160126
10	RAD21	chr2:10160271-10160374	K562	blood:	n/a	n/a
11	USF2	chr2:10160230-10160378	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr2:10160200-10160419	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr2:10160252-10160397	K562	blood:	n/a	n/a
14	CTCF	chr2:10160242-10160418	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr2:10160240-10160390	WERI-Rb-1	eye:	n/a	n/a
16	USF1	chr2:10160216-10160416	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr2:10159562-10160418	K562	blood:	n/a	chr2:10160315-10160326 chr2:10160314-10160329 chr2:10159974-10159981 chr2:10160314-10160327 chr2:10160315-10160324 chr2:10160316-10160326 chr2:10160315-10160326 chr2:10160316-10160326 chr2:10160315-10160325 chr2:10160316-10160325
18	CTCF	chr2:10160236-10160447	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr2:10160306-10160363	GM19238	blood:	n/a	n/a
20	CTCF	chr2:10160310-10160367	Lung_OC	lung:	n/a	n/a
21	CTCF	chr2:10160290-10160406	GM19239	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10159180..10160819-chr2:10275177..10277719,2	K562	blood:
2	chr2:10158217..10160856-chr2:10163800..10165547,2	K562	blood:
3	chr2:10159162..10163514-chr2:10181699..10184437,5	MCF-7	breast:
4	chr2:10158527..10161012-chr2:10168048..10171028,3	K562	blood:
5	chr2:10159210..10161560-chr2:10162271..10163980,2	MCF-7	breast:
6	chr2:10160149..10163716-chr2:10178459..10180847,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260476	TF binding region
ENSG00000260077	Chromatin interaction
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12468647	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12992130	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4669518	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713766	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10156200-10160400	Enhancers	Liver	Liver
2	chr2:10158200-10161000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:10159200-10160400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr2:10159200-10160800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:10159200-10163400	Enhancers	Placenta	Placenta
6	chr2:10159400-10160400	Enhancers	Gastric	stomach
7	chr2:10159400-10160400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:10159400-10160800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:10159400-10161000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:10159600-10160800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:10159800-10161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:10159800-10167600	Weak transcription	Right Atrium	heart
13	chr2:10160000-10161600	Weak transcription	NHEK	skin
14	chr2:10160000-10161800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:10160000-10161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:10160200-10160400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:10160200-10161800	Weak transcription	K562	blood
18	chr2:10160200-10168000	Weak transcription	Spleen	Spleen

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