Variant report

Variant	rs12998277
Chromosome Location	chr2:209228206-209228207
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:209228143-209228672	MCF-7	breast:	n/a	n/a
2	RXRA	chr2:209228190-209228646	SK-N-SH	brain:	n/a	n/a
3	MEF2A	chr2:209228124-209228678	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:209228048-209228804	A549	lung:	n/a	n/a
5	POLR2A	chr2:209228144-209228639	SK-N-SH	brain:	n/a	n/a
6	EP300	chr2:209228111-209228634	SK-N-SH_RA	brain:	n/a	n/a
7	JUN	chr2:209228163-209228623	K562	blood:	n/a	n/a
8	SIN3AK20	chr2:209228082-209228670	MCF-7	breast:	n/a	n/a
9	TEAD4	chr2:209228206-209228654	SK-N-SH	brain:	n/a	n/a
10	JUND	chr2:209228088-209228775	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr2:209228003-209228699	SK-N-SH	brain:	n/a	n/a
12	FOXM1	chr2:209228126-209228603	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr2:209227820-209228805	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr2:209228160-209228430	NHDF-neo	bronchial:	n/a	n/a
15	FOSL2	chr2:209228123-209228794	SK-N-SH	brain:	n/a	n/a
16	EP300	chr2:209228170-209228589	SK-N-SH_RA	brain:	n/a	n/a
17	NFIC	chr2:209228197-209228716	SK-N-SH	brain:	n/a	n/a
18	MAX	chr2:209228188-209228677	SK-N-SH	brain:	n/a	n/a
19	GATA3	chr2:209227807-209228894	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr2:209228013-209228823	MCF-7	breast:	n/a	n/a
21	EBF1	chr2:209228204-209228474	GM12878	blood:	n/a	n/a
22	NFIC	chr2:209228047-209228775	SK-N-SH	brain:	n/a	n/a
23	PBX3	chr2:209227997-209228794	SK-N-SH	brain:	n/a	n/a
24	TCF12	chr2:209227952-209228797	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr2:209227944-209228854	SK-N-SH	brain:	n/a	n/a
26	TEAD4	chr2:209228197-209228597	K562	blood:	n/a	n/a
27	EP300	chr2:209228058-209228730	SK-N-SH	brain:	n/a	n/a
28	JUND	chr2:209228086-209228787	SK-N-SH	brain:	n/a	n/a
29	PBX3	chr2:209228148-209228717	SK-N-SH	brain:	n/a	n/a
30	FOXM1	chr2:209227912-209228789	SK-N-SH	brain:	n/a	n/a
31	JUND	chr2:209228013-209228786	SK-N-SH	brain:	n/a	n/a
32	MAX	chr2:209228152-209228696	SK-N-SH	brain:	n/a	n/a
33	EP300	chr2:209227993-209228721	SK-N-SH	brain:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000213081	TF binding region

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10177810	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10190458	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10206991	0.88[AMR][1000 genomes]
rs11538998	1.00[ASN][1000 genomes]
rs11693993	0.85[EUR][1000 genomes]
rs11885913	1.00[ASN][1000 genomes]
rs11891163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897777	0.88[AMR][1000 genomes]
rs11902124	0.84[AMR][1000 genomes]
rs12991283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397965	0.88[AMR][1000 genomes]
rs13400356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407268	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17699838	1.00[ASN][1000 genomes]
rs17700235	1.00[ASN][1000 genomes]
rs1866046	1.00[ASN][1000 genomes]
rs1898436	0.97[EUR][1000 genomes]
rs1898437	0.86[EUR][1000 genomes]
rs28418905	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28885800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34259292	0.90[AMR][1000 genomes]
rs35217101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35293936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675761	0.97[EUR][1000 genomes]
rs61193569	0.84[AMR][1000 genomes]
rs66826643	1.00[ASN][1000 genomes]
rs6725527	1.00[ASN][1000 genomes]
rs67393765	0.84[AMR][1000 genomes]
rs67660353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67757182	0.84[AMR][1000 genomes]
rs67965883	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72986744	0.84[AMR][1000 genomes]
rs7563597	0.81[AMR][1000 genomes]
rs7608913	0.84[AMR][1000 genomes]
rs999890	1.00[ASN][1000 genomes]
rs999891	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
3	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv437315	chr2:209204714-209249613	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209220200-209229800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:209220200-209235200	Weak transcription	K562	blood
3	chr2:209221800-209231200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:209224800-209234200	Weak transcription	Placenta	Placenta
5	chr2:209225800-209228600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:209226000-209230200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:209226000-209230800	Weak transcription	Spleen	Spleen
8	chr2:209226000-209234200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:209227400-209228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:209227400-209228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:209227400-209229200	Enhancers	NHDF-Ad	bronchial
12	chr2:209227600-209228400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:209227600-209228400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:209227600-209229200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:209227600-209229200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:209227800-209228400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:209227800-209228800	Enhancers	HSMMtube	muscle
18	chr2:209227800-209229000	Enhancers	HMEC	breast
19	chr2:209227800-209229200	Enhancers	NHLF	lung
20	chr2:209228000-209228400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:209228000-209228400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:209228000-209228800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:209228000-209228800	Enhancers	GM12878-XiMat	blood
24	chr2:209228000-209228800	Enhancers	NHEK	skin
25	chr2:209228000-209228800	Enhancers	Osteobl	bone
26	chr2:209228000-209229000	Enhancers	Hela-S3	cervix
27	chr2:209228200-209231200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links