Variant report

Variant	rs9646095
Chromosome Location	chr13:38062758-38062759
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	chr13:38062748-38063318	SK-N-SH	brain:	n/a	chr13:38063025-38063039 chr13:38063213-38063227 chr13:38063260-38063274
2	JUND	chr13:38062732-38063161	SK-N-SH	brain:	n/a	chr13:38062856-38062865
3	GATA3	chr13:38062657-38063460	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr13:38062698-38063342	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr13:38062668-38063378	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LINC01048	TF binding region

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12427956	0.80[EUR][1000 genomes]
rs12427961	0.87[EUR][1000 genomes]
rs12429268	0.87[EUR][1000 genomes]
rs1322796	0.80[EUR][1000 genomes]
rs1407606	0.80[EUR][1000 genomes]
rs1830656	0.80[EUR][1000 genomes]
rs1853325	0.80[EUR][1000 genomes]
rs4941869	0.87[EUR][1000 genomes]
rs7317019	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7327444	0.80[EUR][1000 genomes]
rs7986151	0.80[EUR][1000 genomes]
rs7992636	0.80[EUR][1000 genomes]
rs9532057	0.80[EUR][1000 genomes]
rs9532062	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9532065	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9547854	0.80[EUR][1000 genomes]
rs9547855	0.80[EUR][1000 genomes]
rs9547856	0.80[EUR][1000 genomes]
rs9547857	0.80[EUR][1000 genomes]
rs9547858	0.80[EUR][1000 genomes]
rs9547859	0.80[EUR][1000 genomes]
rs9547860	0.80[EUR][1000 genomes]
rs9547863	0.80[EUR][1000 genomes]
rs9547870	0.80[EUR][1000 genomes]
rs9547874	0.87[EUR][1000 genomes]
rs9547878	0.87[EUR][1000 genomes]
rs9547879	0.85[EUR][1000 genomes]
rs9547881	0.85[EUR][1000 genomes]
rs9547882	0.87[EUR][1000 genomes]
rs9547885	0.87[EUR][1000 genomes]
rs9547886	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9547901	0.90[EUR][1000 genomes]
rs9547903	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9646096	1.00[AMR][1000 genomes];1.00[EUR][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:18 , 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	chr13:38055800-38065200	Weak transcription	HSMMtube	muscle
3	chr13:38056200-38065600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:38058600-38065600	Weak transcription	Fetal Stomach	stomach
5	chr13:38059400-38064600	Enhancers	HSMM	muscle
6	chr13:38059400-38066000	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:38060200-38065600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:38060600-38064400	Weak transcription	Fetal Lung	lung
9	chr13:38060800-38063200	Weak transcription	NHLF	lung
10	chr13:38061400-38070000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:38061800-38066800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:38062000-38064800	Enhancers	Osteobl	bone
13	chr13:38062200-38065000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:38062200-38067800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr13:38062400-38062800	Weak transcription	NH-A	brain
16	chr13:38062400-38062800	Weak transcription	NHDF-Ad	bronchial
17	chr13:38062400-38064800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:38062600-38064800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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