Variant report

Variant	rs17004657
Chromosome Location	chr21:45936499-45936500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:45933564-45938089	HepG2	liver:	n/a	n/a
2	POLR2A	chr21:45934147-45937806	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:45935831-45937681	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr21:45935045-45937816	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:45936466-45936516	HMEC	breast:	n/a
2	chr21:45936466-45936516	ovcar-3	ovarian:	n/a
3	chr21:45936466-45936516	HEK293	kidney:	embryo
4	chr21:45936466-45936516	BJ	skin:	n/a
5	chr21:45936466-45936516	ECC-1	luminal epithelium:	n/a
6	chr21:45936466-45936516	U87	brain:	n/a
7	chr21:45936466-45936516	HCF	heart:	n/a
8	chr21:45936466-45936516	GM06990	blood:	n/a
9	chr21:45936466-45936516	NHDF-neo	bronchial:	n/a
10	chr21:45936466-45936516	NB4	blood:	n/a
11	chr21:45936466-45936516	NH-A	brain:	n/a
12	chr21:45936466-45936516	AG04450	lung:	fetal
13	chr21:45936466-45936516	SK-N-SH	brain:	n/a
14	chr21:45936466-45936516	Hela-S3	cervix:	n/a
15	chr21:45936466-45936516	PFSK-1	brain:	n/a
16	chr21:45936466-45936516	ProgFib	skin:	n/a
17	chr21:45936466-45936516	MCF-7	breast:	n/a
18	chr21:45936466-45936516	GM12892	blood:	n/a
19	chr21:45936466-45936516	GM12891	blood:	n/a
20	chr21:45936466-45936516	AG04449	skin:	fetal
21	chr21:45936466-45936516	AoSMC	blood vessel:	n/a
22	chr21:45936466-45936516	A549	lung:	n/a
23	chr21:45936466-45936516	HIPEpiC	eye:	n/a
24	chr21:45936466-45936516	HCM	heart:	n/a
25	chr21:45936466-45936516	GM19239	blood:	n/a
26	chr21:45936466-45936516	PANC-1	pancreas:	n/a
27	chr21:45936466-45936516	PrEC	prostate:	n/a
28	chr21:45936466-45936516	AG09319	gingival:	n/a
29	chr21:45936466-45936516	IMR90	lung:	fetal
30	chr21:45936466-45936516	HRCEpiC	kidney:	n/a
31	chr21:45936466-45936516	AG10803	skin:	n/a
32	chr21:45936466-45936516	HRPEpiC	eye:	n/a
33	chr21:45936466-45936516	SKMC	muscle:	n/a
34	chr21:45936466-45936516	GM12878	blood:	n/a
35	chr21:45936466-45936516	NT2-D1	testis:	n/a
36	chr21:45936466-45936516	MCF10A-Er-Src	breast:	n/a
37	chr21:45936466-45936516	RPTEC	kidney:	n/a
38	chr21:45936466-45936516	SAEC	small airway:	n/a
39	chr21:45936466-45936516	HRE	kidney:	n/a
40	chr21:45936466-45936516	LNCaP	prostate:	n/a
41	chr21:45936466-45936516	Hepatocyte	liver:	n/a
42	chr21:45936466-45936516	SK-N-SH_RA	brain:	n/a
43	chr21:45936466-45936516	T-47D	breast:	n/a
44	chr21:45936466-45936516	SK-N-MC	brain:	n/a
45	chr21:45936466-45936516	K562	blood:	n/a
46	chr21:45936466-45936516	HCPEpiC	choroid plexus:	n/a
47	chr21:45936466-45936516	H1-hESC	embryonic stem cell:	embryo
48	chr21:45936466-45936516	HPAEpiC	pulmonary alveolar:	n/a
49	chr21:45936466-45936516	BE2_C	brain:	n/a
50	chr21:45936466-45936516	HCT-116	colon:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45933852..45936742-chr21:45938611..45940347,2	K562	blood:
2	chr21:45934556..45936519-chr21:46293000..46295874,2	MCF-7	breast:

No data

Variant related genes	Relation type
C21orf90	TF binding region
C21orf90	CpG island
ENSG00000183255	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17004653	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3788122	1.00[YRI][hapmap]
rs59571442	1.00[AFR][1000 genomes]
rs7284037	1.00[YRI][hapmap]

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	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
3	esv3361489	chr21:45669073-46013747	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
4	nsv913918	chr21:45697755-45941566	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv1058359	chr21:45724055-45941566	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv1065203	chr21:45731690-45941566	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv544473	chr21:45731690-45941566	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv913942	chr21:45740823-45941566	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv913943	chr21:45740823-46031810	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv1067264	chr21:45757599-45941566	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv544474	chr21:45757599-45941566	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv913944	chr21:45757905-45941566	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	nsv913946	chr21:45838632-46031810	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv913948	chr21:45860912-46031810	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1056424	chr21:45894901-46031810	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv544475	chr21:45894901-46031810	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	nsv1055163	chr21:45895663-46031810	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv913949	chr21:45911950-45941566	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45916800-45951600	Weak transcription	Right Atrium	heart
2	chr21:45931200-45936800	Weak transcription	Gastric	stomach
3	chr21:45931200-45937200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:45931200-45937200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr21:45931400-45936800	Weak transcription	Liver	Liver
6	chr21:45931400-45936800	Weak transcription	K562	blood
7	chr21:45931400-45937200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:45931400-45939600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:45931600-45937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr21:45932000-45937400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:45934600-45937400	Enhancers	HepG2	liver
12	chr21:45935200-45937600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:45936400-45936600	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links