Variant report

Variant	rs2773268
Chromosome Location	chr13:52377296-52377297
allele	C/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	MAZ	chr13:52377273-52379024	IMR90	lung:	n/a	chr13:52378145-52378154 chr13:52377651-52377660 chr13:52378145-52378154 chr13:52378013-52378022 chr13:52378144-52378155
2	MTA3	chr13:52377128-52379056	GM12878	blood:	n/a	n/a
3	EBF1	chr13:52377235-52378433	GM12878	blood:	n/a	n/a
4	POLR2A	chr13:52376417-52379808	GM12878	blood:	n/a	n/a
5	CTBP2	chr13:52377240-52379089	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr13:52377115-52379501	GM12878	blood:	n/a	n/a
7	POLR2A	chr13:52377228-52378780	GM18526	blood:	n/a	n/a
8	POLR2A	chr13:52376283-52380704	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr13:52375841-52380503	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr13:52377279-52378848	HepG2	liver:	n/a	chr13:52377338-52377353
11	POLR2A	chr13:52377233-52379204	GM12878	blood:	n/a	n/a
12	RELA	chr13:52377238-52378996	GM15510	blood:	n/a	n/a
13	POLR2A	chr13:52377158-52379132	GM12878	blood:	n/a	n/a
14	POLR2A	chr13:52377217-52379111	GM19193	blood:	n/a	n/a
15	POLR2A	chr13:52377209-52379182	Raji	blood:	n/a	n/a
16	PML	chr13:52377264-52379000	GM12878	blood:	n/a	n/a
17	POLR2A	chr13:52377164-52379718	GM12891	blood:	n/a	n/a
18	STAT1	chr13:52377073-52378592	GM12878	blood:	n/a	chr13:52377949-52377961
19	MAX	chr13:52377268-52378897	H1-hESC	embryonic stem cell:	n/a	chr13:52378145-52378154 chr13:52377651-52377660 chr13:52378145-52378154 chr13:52378013-52378022 chr13:52378144-52378155
20	POLR2A	chr13:52377035-52379461	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr13:52377290-52379341	GM12892	blood:	n/a	n/a
22	POLR2A	chr13:52377016-52379300	GM12892	blood:	n/a	n/a
23	MXI1	chr13:52377162-52378793	GM12878	blood:	n/a	chr13:52377338-52377353
24	ESRRA	chr13:52375899-52379115	GM12878	blood:	n/a	chr13:52376359-52376371 chr13:52376363-52376381 chr13:52376361-52376371 chr13:52376359-52376375
25	POLR2A	chr13:52377156-52379131	HepG2	liver:	n/a	n/a
26	POLR2A	chr13:52377198-52379616	GM12878	blood:	n/a	n/a
27	POLR2A	chr13:52376998-52379884	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
2	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
3	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
4	chr13:52160060..52163108-chr13:52376667..52378456,3	K562	blood:
5	chr13:52157329..52158871-chr13:52376423..52379239,3	K562	blood:
6	chr13:52376169..52378547-chr13:52701514..52703656,2	MCF-7	breast:
7	chr13:52160060..52162638-chr13:52376878..52378456,2	K562	blood:
8	chr13:52376935..52378764-chr13:52436044..52437882,2	MCF-7	breast:
9	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
10	chr13:52156934..52159026-chr13:52376788..52379281,3	K562	blood:
11	chr13:52015156..52017204-chr13:52376088..52377740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231856	TF binding region
ENSG00000236778	Chromatin interaction
ENSG00000197168	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000123171	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760302	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2760303	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2760304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760305	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2773267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2773269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471107	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs512948	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs518210	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs541434	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription 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	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52372200-52377400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:52373200-52377400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:52373600-52377400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:52374000-52377400	Enhancers	Primary hematopoietic stem cells	blood
5	chr13:52374000-52377400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:52374600-52377400	Enhancers	Placenta	Placenta
7	chr13:52374600-52377400	Enhancers	Psoas Muscle	Psoas
8	chr13:52374600-52377600	Enhancers	Lung	lung
9	chr13:52375000-52377400	Enhancers	Right Atrium	heart
10	chr13:52375400-52377400	Enhancers	Pancreas	Pancrea
11	chr13:52375400-52377400	Enhancers	HUVEC	blood vessel
12	chr13:52375600-52377400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:52375600-52377400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:52375600-52377400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:52375600-52377400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:52375600-52377400	Enhancers	Fetal Intestine Large	intestine
17	chr13:52375600-52377400	Enhancers	Left Ventricle	heart
18	chr13:52375600-52377400	Enhancers	Right Ventricle	heart
19	chr13:52375600-52377400	Enhancers	HMEC	breast
20	chr13:52375600-52377400	Enhancers	HSMM	muscle
21	chr13:52375600-52377400	Enhancers	HSMMtube	muscle
22	chr13:52375600-52377600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr13:52375800-52377400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr13:52375800-52377400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:52375800-52377400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr13:52375800-52377400	Enhancers	NHDF-Ad	bronchial
27	chr13:52375800-52377600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:52375800-52377800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:52375800-52377800	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr13:52375800-52377800	Enhancers	Spleen	Spleen
31	chr13:52376000-52377400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr13:52376000-52377400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:52376000-52377400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:52376000-52377400	Enhancers	Aorta	Aorta
35	chr13:52376000-52377600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:52376000-52377800	Flanking Active TSS	Hela-S3	cervix
37	chr13:52376200-52377400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:52376200-52377400	Enhancers	Fetal Lung	lung
39	chr13:52376200-52377600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr13:52376400-52377400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:52376400-52377600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr13:52376400-52377800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr13:52376400-52377800	Flanking Active TSS	GM12878-XiMat	blood
44	chr13:52376600-52377400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr13:52376600-52377400	Enhancers	Brain Substantia Nigra	brain
46	chr13:52376600-52377400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr13:52376600-52377600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:52376600-52377600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr13:52376600-52377600	Weak transcription	Gastric	stomach
50	chr13:52376600-52377600	Weak transcription	Ovary	ovary

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