Variant report

Variant	rs12625297
Chromosome Location	chr20:23416821-23416822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr20:23416442-23416901	HepG2	liver:	n/a	chr20:23416759-23416768
2	RAD21	chr20:23416797-23416837	HepG2	liver:	n/a	n/a
3	YY1	chr20:23416529-23417047	HepG2	liver:	n/a	n/a
4	RCOR1	chr20:23416517-23417044	HepG2	liver:	n/a	n/a
5	EP300	chr20:23416401-23417438	HepG2	liver:	n/a	n/a
6	RFX5	chr20:23416741-23417019	HepG2	liver:	n/a	n/a
7	HEY1	chr20:23416598-23417117	HepG2	liver:	n/a	n/a
8	CEBPB	chr20:23416564-23416889	HepG2	liver:	n/a	n/a
9	FOXA1	chr20:23416522-23417676	HepG2	liver:	n/a	n/a
10	FOXA1	chr20:23416371-23417447	HepG2	liver:	n/a	n/a
11	FOXA2	chr20:23416517-23416985	HepG2	liver:	n/a	n/a
12	FOXA1	chr20:23416458-23417512	HepG2	liver:	n/a	n/a
13	FOXA1	chr20:23416520-23417550	HepG2	liver:	n/a	n/a
14	MAFF	chr20:23416718-23416913	HepG2	liver:	n/a	n/a
15	YY1	chr20:23416489-23417160	HepG2	liver:	n/a	chr20:23417050-23417059
16	NFIC	chr20:23416466-23417156	HepG2	liver:	n/a	n/a
17	MAX	chr20:23416652-23416981	HepG2	liver:	n/a	n/a
18	FOXA2	chr20:23416597-23417111	A549	lung:	n/a	n/a
19	CHD2	chr20:23416624-23416920	HepG2	liver:	n/a	n/a
20	NFIC	chr20:23416405-23417091	HepG2	liver:	n/a	n/a
21	HEY1	chr20:23416612-23417071	HepG2	liver:	n/a	n/a
22	SMC3	chr20:23416606-23416833	HepG2	liver:	n/a	n/a
23	POLR2A	chr20:23416761-23417005	HepG2	liver:	n/a	n/a
24	TBP	chr20:23416584-23417044	HepG2	liver:	n/a	n/a
25	ARID3A	chr20:23416561-23416867	HepG2	liver:	n/a	n/a
26	MAZ	chr20:23416698-23417018	HepG2	liver:	n/a	n/a
27	EP300	chr20:23416615-23417014	HepG2	liver:	n/a	n/a
28	MAFK	chr20:23416640-23416970	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23336129..23338538-chr20:23416708..23418719,2	K562	blood:
2	chr20:23415427..23417677-chr20:23422614..23424382,2	K562	blood:
3	chr20:23342185..23344395-chr20:23415797..23420151,3	K562	blood:
4	chr20:23415648..23417559-chr20:23421207..23423158,2	MCF-7	breast:

No data

Variant related genes	Relation type
CSTL1	TF binding region
ENSG00000232645	Chromatin interaction
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10485644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1076777	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109557	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1122407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12624341	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12625257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625468	0.96[EUR][1000 genomes]
rs12625489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625948	0.80[AMR][1000 genomes]
rs12625959	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12625994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16985266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16985303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16985337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273237	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34036626	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736756	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761278	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs56393556	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56693860	0.96[EUR][1000 genomes]
rs56725318	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57322153	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57535381	0.80[AMR][1000 genomes]
rs57896475	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59852988	0.96[EUR][1000 genomes]
rs60799291	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61024391	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61297472	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61344818	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73901826	0.96[EUR][1000 genomes]
rs73901859	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73901870	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8115832	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8117246	0.96[EUR][1000 genomes]
rs8123389	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8125332	0.96[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	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12625297	CSTL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12625297	CSTL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23415600-23417600	Flanking Active TSS	HepG2	liver
2	chr20:23415800-23417400	Enhancers	Pancreas	Pancrea
3	chr20:23415800-23417800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr20:23415800-23417800	Enhancers	Fetal Muscle Trunk	muscle
5	chr20:23416400-23417200	Enhancers	Right Ventricle	heart
6	chr20:23416400-23417400	Flanking Active TSS	Liver	Liver
7	chr20:23416400-23417600	Enhancers	Brain Angular Gyrus	brain
8	chr20:23416400-23417600	Enhancers	Fetal Brain Male	brain
9	chr20:23416400-23417600	Enhancers	Fetal Brain Female	brain
10	chr20:23416400-23417800	Enhancers	Fetal Intestine Small	intestine
11	chr20:23416400-23417800	Enhancers	Stomach Mucosa	stomach
12	chr20:23416600-23417000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:23416600-23417200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr20:23416600-23417200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr20:23416600-23417200	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr20:23416600-23417200	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr20:23416600-23417200	Enhancers	Placenta	Placenta
18	chr20:23416600-23417200	Enhancers	Fetal Stomach	stomach
19	chr20:23416600-23417200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr20:23416600-23417400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr20:23416600-23417400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr20:23416600-23417400	Enhancers	Fetal Lung	lung
23	chr20:23416600-23417600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr20:23416600-23417600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr20:23416600-23417600	Enhancers	Fetal Muscle Leg	muscle
26	chr20:23416600-23417600	Enhancers	Left Ventricle	heart
27	chr20:23416600-23417800	Enhancers	Right Atrium	heart
28	chr20:23416800-23417000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr20:23416800-23417000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:23416800-23417000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:23416800-23417200	Enhancers	Gastric	stomach
32	chr20:23416800-23417200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr20:23416800-23417600	Enhancers	Colonic Mucosa	Colon
34	chr20:23416800-23417600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr20:23416800-23417800	Enhancers	Fetal Intestine Large	intestine
36	chr20:23416800-23417800	Enhancers	Ovary	ovary

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