Variant report

Variant	rs16985354
Chromosome Location	chr20:23417364-23417365
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	ATF1	chr20:23417323-23417566	K562	blood:	n/a	n/a
2	EP300	chr20:23416401-23417438	HepG2	liver:	n/a	n/a
3	ELF1	chr20:23417359-23417620	HepG2	liver:	n/a	chr20:23417476-23417489 chr20:23417540-23417553 chr20:23417542-23417553
4	JUND	chr20:23417362-23417589	K562	blood:	n/a	n/a
5	FOXA1	chr20:23416522-23417676	HepG2	liver:	n/a	n/a
6	FOXA1	chr20:23416371-23417447	HepG2	liver:	n/a	n/a
7	FOXA1	chr20:23416458-23417512	HepG2	liver:	n/a	n/a
8	FOXA1	chr20:23416520-23417550	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:23417350-23417472	K562	blood:	n/a	n/a
10	EP300	chr20:23417313-23417554	K562	blood:	n/a	chr20:23417478-23417487
11	FOXA2	chr20:23417056-23417571	HepG2	liver:	n/a	n/a
12	ELF1	chr20:23417325-23417709	K562	blood:	n/a	chr20:23417476-23417489 chr20:23417540-23417553 chr20:23417542-23417553
13	RCOR1	chr20:23417249-23417568	K562	blood:	n/a	n/a

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:

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12106211	1.00[YRI][hapmap]
rs16985269	0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs16985333	0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs6132617	1.00[YRI][hapmap]
rs7272812	1.00[YRI][hapmap];0.83[AFR][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

No data

Chromatin state (count:28 , 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	chr20:23416400-23417400	Flanking Active TSS	Liver	Liver
6	chr20:23416400-23417600	Enhancers	Brain Angular Gyrus	brain
7	chr20:23416400-23417600	Enhancers	Fetal Brain Male	brain
8	chr20:23416400-23417600	Enhancers	Fetal Brain Female	brain
9	chr20:23416400-23417800	Enhancers	Fetal Intestine Small	intestine
10	chr20:23416400-23417800	Enhancers	Stomach Mucosa	stomach
11	chr20:23416600-23417400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr20:23416600-23417400	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr20:23416600-23417400	Enhancers	Fetal Lung	lung
14	chr20:23416600-23417600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr20:23416600-23417600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:23416600-23417600	Enhancers	Fetal Muscle Leg	muscle
17	chr20:23416600-23417600	Enhancers	Left Ventricle	heart
18	chr20:23416600-23417800	Enhancers	Right Atrium	heart
19	chr20:23416800-23417600	Enhancers	Colonic Mucosa	Colon
20	chr20:23416800-23417600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr20:23416800-23417800	Enhancers	Fetal Intestine Large	intestine
22	chr20:23416800-23417800	Enhancers	Ovary	ovary
23	chr20:23417000-23417600	Enhancers	K562	blood
24	chr20:23417000-23422800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:23417200-23417600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr20:23417200-23417600	Enhancers	Brain Anterior Caudate	brain
27	chr20:23417200-23417800	Enhancers	Brain Cingulate Gyrus	brain
28	chr20:23417200-23434800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links