Variant report

Variant	rs59305213
Chromosome Location	chr21:17442585-17442586
allele	A/G
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	CTCF	chr21:17442560-17442710	HAc	cerebellar:	n/a	n/a
2	CTCF	chr21:17442560-17442710	HA-sp	spinal cord:	n/a	n/a
3	CTCF	chr21:17442520-17442670	AG09319	gingival:	n/a	n/a
4	FOXA1	chr21:17442456-17442767	T-47D	breast:	n/a	n/a
5	CTCF	chr21:17442520-17442670	AG10803	skin:	n/a	n/a
6	EP300	chr21:17442414-17442952	SK-N-SH_RA	brain:	n/a	chr21:17442640-17442654 chr21:17442634-17442642
7	CTCF	chr21:17442500-17442650	NHEK	skin:	n/a	n/a
8	CTCF	chr21:17442519-17442706	Gliobla	brain:	n/a	n/a
9	CTCF	chr21:17442540-17442690	HEEpiC	esophagus:	n/a	n/a
10	CTCF	chr21:17442520-17442670	HFF-Myc	foreskin:	n/a	n/a
11	FOXP2	chr21:17442433-17442781	SK-N-MC	brain:	n/a	n/a
12	CTCF	chr21:17442480-17442630	AoAF	blood vessel:	n/a	n/a
13	CTCF	chr21:17442540-17442690	HAc	cerebellar:	n/a	n/a
14	TAF1	chr21:17442540-17443077	PFSK-1	brain:	n/a	n/a
15	EP300	chr21:17442486-17442991	SK-N-SH_RA	brain:	n/a	chr21:17442640-17442654 chr21:17442634-17442642
16	CTCF	chr21:17442540-17442690	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr21:17442520-17442670	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr21:17442500-17442650	AG10803	skin:	n/a	n/a
19	YY1	chr21:17442422-17442957	SK-N-SH_RA	brain:	n/a	n/a
20	GATA2	chr21:17442412-17443768	SH-SY5Y	brain:	n/a	n/a
21	POLR2A	chr21:17442331-17444053	PFSK-1	brain:	n/a	n/a
22	CEBPB	chr21:17442502-17442706	MCF-7	breast:	n/a	n/a
23	MXI1	chr21:17441476-17443970	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr21:17442500-17442650	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr21:17442480-17442630	NHDF-neo	bronchial:	n/a	n/a
26	CTCF	chr21:17442580-17442730	BJ	skin:	n/a	n/a
27	CTCF	chr21:17442500-17442650	HCPEpiC	choroid plexus:	n/a	n/a
28	CTCF	chr21:17442480-17442630	HMF	breast:	n/a	n/a
29	CTCF	chr21:17442480-17442630	HVMF	connective:	n/a	n/a
30	CTCF	chr21:17442533-17442665	LNCaP	prostate:	n/a	n/a
31	CTCF	chr21:17442460-17442610	MCF-7	breast:	n/a	n/a
32	CTCF	chr21:17442520-17442670	AG04449	skin:	n/a	n/a
33	SIN3AK20	chr21:17442528-17442991	PFSK-1	brain:	n/a	n/a
34	CTCF	chr21:17442500-17442650	AoAF	blood vessel:	n/a	n/a
35	FOXA1	chr21:17442427-17442769	T-47D	breast:	n/a	n/a
36	CTCF	chr21:17442520-17442670	HFF	foreskin:	n/a	n/a
37	GATA3	chr21:17442305-17442767	SH-SY5Y	brain:	n/a	n/a
38	CTCF	chr21:17442560-17442710	SK-N-SH_RA	brain:	n/a	n/a
39	EP300	chr21:17441902-17444931	SK-N-SH	brain:	n/a	chr21:17442640-17442654 chr21:17443209-17443219 chr21:17442634-17442642 chr21:17442984-17442998
40	CTCF	chr21:17442500-17442650	BJ	skin:	n/a	n/a
41	CTCF	chr21:17442542-17442639	ProgFib	skin:	n/a	n/a
42	CTCF	chr21:17442500-17442650	HBMEC	blood vessel:	n/a	n/a
43	POLR2A	chr21:17442391-17443194	PFSK-1	brain:	n/a	n/a
44	CTCF	chr21:17442500-17442650	MCF-7	breast:	n/a	n/a
45	CTCF	chr21:17442540-17442690	HA-sp	spinal cord:	n/a	n/a
46	POLR2A	chr21:17442543-17443083	U87	brain:	n/a	n/a
47	CTCF	chr21:17442516-17442667	Medullo	brain:	n/a	n/a
48	CTCF	chr21:17442500-17442650	BE2_C	brain:	n/a	n/a
49	CTCF	chr21:17442460-17442610	AG09309	skin:	n/a	n/a
50	CTCF	chr21:17442500-17442650	AG04449	skin:	n/a	n/a

Variant related genes	Relation type
LINC00478	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs55954827	1.00[AFR][1000 genomes]
rs73894712	1.00[AFR][1000 genomes]
rs73894740	1.00[AFR][1000 genomes]
rs73894742	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913414	chr21:17383785-17459507	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv913415	chr21:17400916-17452276	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2830060	chr21:17400916-17459507	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv527854	chr21:17400916-17459507	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1851038	chr21:17412144-17488119	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr21:17441400-17444000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17441600-17445000	Active TSS	Brain Germinal Matrix	brain
3	chr21:17441600-17446800	Active TSS	Fetal Brain Female	brain
4	chr21:17441800-17442600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr21:17441800-17443200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr21:17441800-17445400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:17442000-17442800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:17442000-17446200	Active TSS	Brain Angular Gyrus	brain
9	chr21:17442000-17446400	Active TSS	Brain Cingulate Gyrus	brain
10	chr21:17442000-17446800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr21:17442000-17447200	Active TSS	Fetal Brain Male	brain
12	chr21:17442000-17448000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr21:17442200-17442600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:17442200-17442600	Enhancers	Brain Hippocampus Middle	brain
15	chr21:17442200-17442600	Enhancers	NHDF-Ad	bronchial
16	chr21:17442400-17442600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr21:17442400-17442600	Active TSS	NH-A	brain
18	chr21:17442400-17442800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr21:17442400-17443000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:17442400-17443000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:17442400-17443600	Flanking Active TSS	Osteobl	bone
22	chr21:17442400-17443800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:17442400-17443800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr21:17442400-17446200	Active TSS	Brain Anterior Caudate	brain
25	chr21:17442400-17446200	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links