Variant report

Variant	rs9309255
Chromosome Location	chr2:54773841-54773842
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:54772688-54774009	HepG2	liver:	n/a	n/a
2	TAL1	chr2:54773609-54774014	K562	blood:	n/a	n/a
3	STAT3	chr2:54773727-54774067	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr2:54773470-54773946	K562	blood:	n/a	n/a
5	MYC	chr2:54773655-54774104	K562	blood:	n/a	n/a
6	MBD4	chr2:54772724-54774037	HepG2	liver:	n/a	n/a
7	IRF1	chr2:54773660-54774398	K562	blood:	n/a	n/a
8	IRF1	chr2:54773815-54774449	K562	blood:	n/a	n/a
9	FOXA2	chr2:54772416-54773865	HepG2	liver:	n/a	n/a
10	EP300	chr2:54772698-54773950	HepG2	liver:	n/a	n/a
11	JUND	chr2:54773713-54774020	K562	blood:	n/a	n/a
12	TBL1XR1	chr2:54773739-54773989	K562	blood:	n/a	n/a
13	CUX1	chr2:54773781-54774098	K562	blood:	n/a	n/a
14	RCOR1	chr2:54773657-54774005	K562	blood:	n/a	n/a
15	TEAD4	chr2:54773612-54774017	K562	blood:	n/a	n/a
16	MYC	chr2:54773801-54774001	K562	blood:	n/a	n/a
17	ARID3A	chr2:54772824-54773842	HepG2	liver:	n/a	n/a
18	TEAD4	chr2:54773551-54774038	K562	blood:	n/a	n/a
19	RCOR1	chr2:54773642-54774085	K562	blood:	n/a	n/a
20	NFIC	chr2:54772704-54773883	HepG2	liver:	n/a	n/a
21	ARID3A	chr2:54773647-54774065	K562	blood:	n/a	n/a
22	TEAD4	chr2:54772696-54773896	HepG2	liver:	n/a	n/a
23	EP300	chr2:54773684-54773914	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234943	TF binding region
ENSG00000228108	Chromatin interaction

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

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

rs_ID	r²[population]
rs10165641	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027950	0.82[CEU][hapmap]
rs1052788	0.80[CEU][hapmap]
rs1052820	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs1112919	1.00[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12463484	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467653	0.84[EUR][1000 genomes]
rs12473338	0.81[EUR][1000 genomes]
rs12475598	0.85[EUR][1000 genomes]
rs12476489	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12477376	0.87[EUR][1000 genomes]
rs12622708	0.93[EUR][1000 genomes]
rs13387476	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17045941	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs17416284	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs3817163	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap]
rs4283459	0.87[EUR][1000 genomes]
rs4519565	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4567979	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671223	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs4671224	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671227	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671229	0.82[CEU][hapmap]
rs4671952	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671959	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4671965	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs60294349	0.85[EUR][1000 genomes]
rs6545428	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545433	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6705756	0.92[CEU][hapmap]
rs6717713	0.81[EUR][1000 genomes]
rs6717816	0.81[EUR][1000 genomes]
rs6738725	0.84[CEU][hapmap]
rs6739099	0.87[EUR][1000 genomes]
rs67457439	0.81[EUR][1000 genomes]
rs68134840	0.95[EUR][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
10	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:54768400-54775800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:54769800-54775400	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:54769800-54775600	Weak transcription	Fetal Stomach	stomach
14	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
15	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
16	chr2:54770400-54775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:54770400-54775400	Weak transcription	Lung	lung
18	chr2:54770400-54776800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:54770600-54775400	Weak transcription	Right Atrium	heart
21	chr2:54770600-54776800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
23	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:54772400-54774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:54772600-54774000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:54772600-54774000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:54772600-54774000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:54772600-54774000	Enhancers	Fetal Heart	heart
29	chr2:54772600-54774000	Enhancers	Stomach Mucosa	stomach
30	chr2:54772600-54774000	Flanking Active TSS	A549	lung
31	chr2:54772600-54774000	Enhancers	HUVEC	blood vessel
32	chr2:54772600-54774000	Enhancers	Osteobl	bone
33	chr2:54772600-54774200	Enhancers	Brain Hippocampus Middle	brain
34	chr2:54772600-54774200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:54772600-54774200	Enhancers	HMEC	breast
36	chr2:54772600-54774200	Enhancers	NHDF-Ad	bronchial
37	chr2:54772600-54774600	Enhancers	Brain Substantia Nigra	brain
38	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
39	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
40	chr2:54772800-54774000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:54772800-54774000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:54772800-54774000	Enhancers	Adipose Nuclei	Adipose
43	chr2:54772800-54774000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:54772800-54774000	Enhancers	Spleen	Spleen
45	chr2:54772800-54774200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:54772800-54774200	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:54772800-54774400	Enhancers	Brain Angular Gyrus	brain
48	chr2:54772800-54774400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:54772800-54774400	Enhancers	K562	blood
50	chr2:54772800-54774600	Enhancers	Duodenum Smooth Muscle	Duodenum

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