Variant report

Variant	rs13438746
Chromosome Location	chr7:7575662-7575663
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	NFIC	chr7:7575174-7575860	ECC-1	luminal epithelium:	n/a	chr7:7575416-7575432 chr7:7575414-7575442
2	EP300	chr7:7575228-7575858	ECC-1	luminal epithelium:	n/a	chr7:7575397-7575406
3	NFIC	chr7:7575191-7575785	ECC-1	luminal epithelium:	n/a	chr7:7575416-7575432 chr7:7575414-7575442

Variant related genes	Relation type
COL28A1	TF binding region

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10085695	1.00[MEX][hapmap]
rs10224056	1.00[EUR][1000 genomes]
rs10226571	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237013	1.00[ASW][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10244757	1.00[EUR][1000 genomes]
rs10246969	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10247234	1.00[TSI][hapmap]
rs10249422	1.00[MEX][hapmap]
rs10254036	1.00[EUR][1000 genomes]
rs10257279	1.00[EUR][1000 genomes]
rs10267405	1.00[MEX][hapmap]
rs10269241	0.90[AMR][1000 genomes]
rs10273001	1.00[EUR][1000 genomes]
rs10275145	1.00[MEX][hapmap]
rs10276699	1.00[TSI][hapmap]
rs10279481	0.90[AMR][1000 genomes]
rs10280185	1.00[MEX][hapmap]
rs10280723	1.00[MEX][hapmap]
rs12333875	1.00[MEX][hapmap]
rs17168622	1.00[EUR][1000 genomes]
rs17169196	1.00[MEX][hapmap]
rs2348340	1.00[EUR][1000 genomes]
rs28422034	1.00[EUR][1000 genomes]
rs28488380	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564742	1.00[EUR][1000 genomes]
rs28602361	1.00[EUR][1000 genomes]
rs28706886	1.00[EUR][1000 genomes]
rs28866201	0.90[AMR][1000 genomes]
rs56845168	1.00[EUR][1000 genomes]
rs57830645	1.00[EUR][1000 genomes]
rs60663837	1.00[EUR][1000 genomes]
rs61285017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73349819	1.00[EUR][1000 genomes]
rs73349821	1.00[EUR][1000 genomes]
rs73349832	1.00[EUR][1000 genomes]
rs73353651	1.00[EUR][1000 genomes]
rs7805479	1.00[MEX][hapmap]
rs7808158	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7808619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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
14	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7570200-7579800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:7575200-7577000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr7:7575400-7575800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:7575400-7575800	Flanking Active TSS	Fetal Kidney	kidney
5	chr7:7575400-7575800	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr7:7575400-7576000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:7575600-7575800	Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links