Variant report

Variant	rs17521904
Chromosome Location	chr7:7563941-7563942
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	FOS	chr7:7563821-7564040	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7562049..7564854-chr7:7565202..7567272,2	MCF-7	breast:
2	chr7:7560179..7562918-chr7:7563350..7565628,2	K562	blood:
3	chr7:7556776..7558526-chr7:7562736..7564916,2	MCF-7	breast:

Variant related genes	Relation type
COL28A1	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10234567	1.00[CHB][hapmap]
rs10235484	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10257643	1.00[CHB][hapmap]
rs10276699	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486164	1.00[JPT][hapmap]
rs10486183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486184	0.83[AMR][1000 genomes]
rs11972066	0.86[EUR][1000 genomes]
rs11984435	0.86[EUR][1000 genomes]
rs12666084	0.86[EUR][1000 genomes]
rs12666106	0.86[EUR][1000 genomes]
rs12666212	0.86[EUR][1000 genomes]
rs12669035	0.86[EUR][1000 genomes]
rs12670328	0.86[EUR][1000 genomes]
rs12671201	0.86[EUR][1000 genomes]
rs12671418	0.86[EUR][1000 genomes]
rs12672583	0.86[EUR][1000 genomes]
rs17167726	0.86[EUR][1000 genomes]
rs17167748	0.86[EUR][1000 genomes]
rs17167774	0.86[EUR][1000 genomes]
rs17167927	0.86[EUR][1000 genomes]
rs17168704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169036	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs17457863	0.86[EUR][1000 genomes]
rs17459718	0.86[EUR][1000 genomes]
rs17459836	0.86[EUR][1000 genomes]
rs17459995	0.86[EUR][1000 genomes]
rs17460037	0.86[EUR][1000 genomes]
rs17461022	0.86[EUR][1000 genomes]
rs17461446	0.86[EUR][1000 genomes]
rs17461474	0.86[EUR][1000 genomes]
rs17461538	0.86[EUR][1000 genomes]
rs17462749	0.86[EUR][1000 genomes]
rs17462946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464197	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17464497	1.00[AMR][1000 genomes]
rs17464517	1.00[AMR][1000 genomes]
rs17464585	1.00[AMR][1000 genomes]
rs17465493	1.00[AMR][1000 genomes]
rs17516587	0.86[EUR][1000 genomes]
rs17516628	0.86[EUR][1000 genomes]
rs17516739	0.86[EUR][1000 genomes]
rs17517530	0.86[EUR][1000 genomes]
rs17518933	0.86[EUR][1000 genomes]
rs17519339	0.86[EUR][1000 genomes]
rs17519423	0.86[EUR][1000 genomes]
rs17519676	0.86[EUR][1000 genomes]
rs17520004	0.86[EUR][1000 genomes]
rs17520619	0.86[EUR][1000 genomes]
rs17520689	0.86[EUR][1000 genomes]
rs17521499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521779	0.86[EUR][1000 genomes]
rs17521814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522036	0.86[EUR][1000 genomes]
rs17522077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522279	0.86[EUR][1000 genomes]
rs17522625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522950	0.86[EUR][1000 genomes]
rs17523400	0.86[EUR][1000 genomes]
rs1860726	0.86[EUR][1000 genomes]
rs1922629	0.86[EUR][1000 genomes]
rs1978190	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2191815	0.86[EUR][1000 genomes]
rs34330034	0.86[EUR][1000 genomes]
rs35473859	0.86[EUR][1000 genomes]
rs35772304	0.86[EUR][1000 genomes]
rs3757531	1.00[ASN][1000 genomes]
rs3757532	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs60654515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957976	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6969871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73674556	0.86[EUR][1000 genomes]
rs7778775	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs7782178	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	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
3	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv606043	chr7:7473563-7571420	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7528600-7575400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7561800-7569200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:7563000-7564600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:7563200-7564200	Enhancers	NHDF-Ad	bronchial
5	chr7:7563200-7564400	Enhancers	Osteobl	bone
6	chr7:7563400-7564000	Enhancers	Fetal Intestine Large	intestine
7	chr7:7563400-7564200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:7563400-7564400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:7563600-7564000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:7563600-7564200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:7563800-7564000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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