Variant report

Variant	rs60654515
Chromosome Location	chr7:7592144-7592145
allele	A/C
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	MAFF	chr7:7591871-7592177	HepG2	liver:	n/a	chr7:7592014-7592032 chr7:7592020-7592034
2	MAFK	chr7:7591853-7592205	HepG2	liver:	n/a	chr7:7592016-7592027 chr7:7592020-7592034 chr7:7592016-7592031 chr7:7592017-7592037 chr7:7592017-7592028 chr7:7592015-7592029 chr7:7592016-7592027 chr7:7592019-7592035
3	MAFK	chr7:7591972-7592165	Hela-S3	cervix:	n/a	chr7:7592016-7592027 chr7:7592020-7592034 chr7:7592016-7592031 chr7:7592017-7592037 chr7:7592017-7592028 chr7:7592015-7592029 chr7:7592016-7592027 chr7:7592019-7592035
4	MAFK	chr7:7591870-7592153	HepG2	liver:	n/a	chr7:7592016-7592027 chr7:7592020-7592034 chr7:7592016-7592031 chr7:7592017-7592037 chr7:7592017-7592028 chr7:7592015-7592029 chr7:7592016-7592027 chr7:7592019-7592035
5	MAFF	chr7:7591911-7592151	K562	blood:	n/a	chr7:7592014-7592032 chr7:7592020-7592034
6	MAFK	chr7:7591872-7592197	IMR90	lung:	n/a	chr7:7592016-7592027 chr7:7592020-7592034 chr7:7592016-7592031 chr7:7592017-7592037 chr7:7592017-7592028 chr7:7592015-7592029 chr7:7592016-7592027 chr7:7592019-7592035

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
2	chr7:7588174..7592470-chr7:7605427..7608009,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL28A1-1	chr7:7591790-7592553	XLOC_006350
2	lnc-COL28A1-1	chr7:7591790-7592553	XLOC_006350
3	lnc-COL28A1-1	chr7:7591790-7592553	XLOC_006350
4	lnc-COL28A1-1	chr7:7591790-7592553	NR_110084
5	lnc-COL28A1-1	chr7:7592093-7592553	ENSG00000272894.1

Variant related genes	Relation type
ENSG00000272732	TF binding region
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10235484	0.87[EUR][1000 genomes]
rs10276699	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486183	0.98[AFR][1000 genomes];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]
rs17151551	0.92[AFR][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]
rs17168444	0.92[AFR][1000 genomes]
rs17168526	0.92[AFR][1000 genomes]
rs17168704	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169036	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[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]
rs17521904	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	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[ASN][1000 genomes]
rs58901081	0.98[AFR][1000 genomes]
rs6956575	0.98[AFR][1000 genomes]
rs6957976	1.00[ASN][1000 genomes]
rs6969871	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73674556	0.86[EUR][1000 genomes]
rs7778775	0.83[AMR][1000 genomes]
rs7782178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783489	1.00[AFR][1000 genomes]
rs7791080	1.00[AFR][1000 genomes]
rs7796098	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
16	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7575800-7593000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7581800-7595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:7588000-7592200	Weak transcription	HSMM	muscle
4	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:7589800-7596000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:7589800-7596000	Weak transcription	Aorta	Aorta
7	chr7:7589800-7596000	Weak transcription	Placenta	Placenta
8	chr7:7589800-7596600	Weak transcription	Gastric	stomach
9	chr7:7590000-7593600	Weak transcription	Brain Angular Gyrus	brain
10	chr7:7590000-7595000	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
12	chr7:7590000-7606200	Weak transcription	Ovary	ovary
13	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
14	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:7590600-7593000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:7591200-7592400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:7591800-7592800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr7:7591800-7593000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:7591800-7593600	Weak transcription	Pancreas	Pancrea
20	chr7:7591800-7594800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:7592000-7592400	Weak transcription	Psoas Muscle	Psoas
22	chr7:7592000-7593200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:7592000-7593800	Weak transcription	Liver	Liver
24	chr7:7592000-7594200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr7:7592000-7596400	Weak transcription	Lung	lung

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