Variant report

Variant	rs55693723
Chromosome Location	chr2:234265403-234265404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234263905-234266140	GM12891	blood:	n/a	n/a
2	GATA3	chr2:234264941-234265430	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234163205..234166188-chr2:234263952..234265730,2	MCF-7	breast:
2	chr2:234195095..234197515-chr2:234263227..234265841,2	MCF-7	breast:
3	chr2:234242282..234244298-chr2:234262922..234265541,2	MCF-7	breast:
4	chr2:234263404..234265699-chr2:234319043..234321996,3	MCF-7	breast:
5	chr2:234264990..234266555-chr2:234275771..234278254,2	K562	blood:
6	chr2:234263725..234265766-chr2:234287688..234290576,3	MCF-7	breast:
7	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
8	chr2:234264479..234266031-chr2:234270714..234272402,2	K562	blood:
9	chr2:234159288..234161886-chr2:234264094..234265602,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259793	TF binding region
ENSG00000251791	Chromatin interaction
ENSG00000130561	Chromatin interaction
ENSG00000201013	Chromatin interaction
ENSG00000085978	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10153744	0.83[ASN][1000 genomes]
rs1046976	0.86[EUR][1000 genomes]
rs11675531	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384918	0.86[EUR][1000 genomes]
rs13420688	0.86[EUR][1000 genomes]
rs55684040	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55804614	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893802	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55983182	0.83[ASN][1000 genomes]
rs56082182	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56405280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58280122	0.95[EUR][1000 genomes]
rs6431364	0.83[ASN][1000 genomes]
rs6722763	0.83[ASN][1000 genomes]
rs6759246	0.83[ASN][1000 genomes]
rs72978363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978374	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978375	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72980318	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7566221	0.83[ASN][1000 genomes]
rs7573866	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576633	0.83[ASN][1000 genomes]
rs7580412	0.83[ASN][1000 genomes]
rs7598771	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv1796836	chr2:234263212-234266842	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv1820563	chr2:234263212-234282210	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234263800-234266200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr2:234263800-234268400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr2:234263800-234268400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr2:234264000-234266000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr2:234264000-234266000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr2:234264000-234266000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr2:234264000-234266000	Transcr. at gene 5' and 3'	A549	lung
8	chr2:234264000-234266000	Flanking Active TSS	GM12878-XiMat	blood
9	chr2:234264000-234267800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:234264200-234266000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:234264200-234266000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:234264200-234266600	Enhancers	Spleen	Spleen
13	chr2:234264400-234265600	Enhancers	Fetal Muscle Leg	muscle
14	chr2:234264400-234265800	Enhancers	Brain Substantia Nigra	brain
15	chr2:234264400-234265800	Enhancers	HMEC	breast
16	chr2:234264400-234266000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:234264400-234266000	Enhancers	Liver	Liver
18	chr2:234264400-234266000	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:234264400-234266000	Enhancers	Left Ventricle	heart
20	chr2:234264400-234266000	Enhancers	Pancreas	Pancrea
21	chr2:234264400-234266000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:234264400-234266000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:234264400-234266400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:234264400-234266600	Enhancers	Gastric	stomach
25	chr2:234264400-234266600	Enhancers	Lung	lung
26	chr2:234264400-234266600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:234264400-234267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:234264400-234268800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:234264400-234268800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:234264400-234269000	Weak transcription	NHLF	lung
31	chr2:234264400-234269600	Weak transcription	Aorta	Aorta
32	chr2:234264400-234274800	Weak transcription	NHDF-Ad	bronchial
33	chr2:234264400-234287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:234264600-234265600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:234264600-234265800	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:234264600-234265800	Enhancers	Fetal Heart	heart
37	chr2:234264600-234265800	Enhancers	Fetal Lung	lung
38	chr2:234264600-234266000	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:234264600-234266000	Enhancers	Stomach Mucosa	stomach
40	chr2:234264600-234266400	Enhancers	Fetal Brain Male	brain
41	chr2:234264600-234266600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:234264600-234266600	Enhancers	Fetal Thymus	thymus
43	chr2:234264600-234266600	Enhancers	Small Intestine	intestine
44	chr2:234264600-234267400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:234264600-234267400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:234264600-234267600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:234264600-234272400	Weak transcription	HUVEC	blood vessel
48	chr2:234264600-234290800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:234264800-234265600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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