Variant report

Variant	rs17055871
Chromosome Location	chr13:38059841-38059842
allele	A/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	EP300	chr13:38059839-38060162	SK-N-SH_RA	brain:	n/a	n/a
2	GATA3	chr13:38059732-38060238	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr13:38059676-38060349	SK-N-SH	brain:	n/a	chr13:38060336-38060343
4	PBX3	chr13:38059744-38060282	SK-N-SH	brain:	n/a	n/a
5	EP300	chr13:38059791-38060174	SK-N-SH_RA	brain:	n/a	n/a
6	NFIC	chr13:38059740-38060371	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LINC01048	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1107244	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584046	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12584670	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322804	0.88[ASN][1000 genomes]
rs1570387	1.00[ASN][1000 genomes]
rs1590305	0.87[ASN][1000 genomes]
rs17055629	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923716	0.86[ASN][1000 genomes]
rs2224659	0.88[ASN][1000 genomes]
rs2323487	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764077	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764078	0.95[ASN][1000 genomes]
rs55903929	0.88[ASN][1000 genomes]
rs56098078	0.87[ASN][1000 genomes]
rs58722541	0.90[ASN][1000 genomes]
rs61946575	0.98[ASN][1000 genomes]
rs61946576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61946592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61946593	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61947266	0.90[ASN][1000 genomes]
rs61947269	0.90[ASN][1000 genomes]
rs6563550	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563551	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73180681	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324216	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334752	0.86[ASN][1000 genomes]
rs7337526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338422	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7984882	0.85[ASN][1000 genomes]
rs7986069	0.84[ASN][1000 genomes]
rs7994129	0.85[ASN][1000 genomes]
rs7995332	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875082	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547877	0.87[ASN][1000 genomes]
rs9576269	0.87[ASN][1000 genomes]
rs9576280	0.84[ASW][hapmap]
rs9594204	0.84[ASN][1000 genomes]
rs9594212	0.87[ASN][1000 genomes]
rs9594214	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603185	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603186	0.86[ASN][1000 genomes]
rs9603191	0.86[ASN][1000 genomes]
rs9603194	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603195	0.88[ASN][1000 genomes]
rs9603210	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9603213	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603214	0.98[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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv899994	chr13:37816086-38087145	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer 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
5	nsv832582	chr13:37943056-38124252	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38053600-38063600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:38055800-38060000	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:38055800-38065200	Weak transcription	HSMMtube	muscle
4	chr13:38056200-38065600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:38056400-38061600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:38057800-38060000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:38058000-38060000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:38058200-38060000	Enhancers	Osteobl	bone
9	chr13:38058600-38060200	Weak transcription	NHLF	lung
10	chr13:38058600-38065600	Weak transcription	Fetal Stomach	stomach
11	chr13:38059400-38060000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr13:38059400-38060200	Enhancers	Ovary	ovary
13	chr13:38059400-38064600	Enhancers	HSMM	muscle
14	chr13:38059400-38066000	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:38059600-38060200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:38059800-38060000	Enhancers	Fetal Lung	lung
17	chr13:38059800-38060200	Enhancers	Adipose Nuclei	Adipose
18	chr13:38059800-38060200	Enhancers	NHDF-Ad	bronchial
19	chr13:38059800-38060800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:38059800-38060800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:38059800-38060800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:38059800-38061200	Enhancers	NH-A	brain

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