Variant report

Variant	rs564779
Chromosome Location	chr21:44785422-44785423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
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	ESR1	chr21:44785381-44785789	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr21:44785342-44785728	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr21:44784564-44785447	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr21:44784653-44785793	ECC-1	luminal epithelium:	n/a	chr21:44785605-44785622

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:44785083..44788037-chr21:44788095..44789736,2	MCF-7	breast:
2	chr21:44781106..44783357-chr21:44784005..44786797,3	K562	blood:
3	chr21:44780314..44782548-chr21:44784562..44786888,3	MCF-7	breast:
4	chr21:44784945..44787524-chr21:44806309..44807951,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYAA-2	chr21:44783212-44785567	XLOC_013961

No data

Variant related genes	Relation type
ENSG00000237989	TF binding region
ENSG00000237989	Chromatin interaction
ENSG00000225637	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2073428	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478075	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs535024	0.90[CHB][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs559480	1.00[YRI][hapmap]
rs565629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs580007	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs587329	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs622330	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs634978	0.87[TSI][hapmap]
rs666249	0.98[ASN][1000 genomes]
rs666699	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs672929	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs672948	0.85[TSI][hapmap]
rs673220	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857566	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857567	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857569	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][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	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	nsv913845	chr21:44781356-44874702	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
18	nsv470901	chr21:44781356-44884252	Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
2	chr21:44780200-44788400	Enhancers	Spleen	Spleen
3	chr21:44782200-44791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr21:44782400-44789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr21:44782600-44785600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr21:44782600-44785600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr21:44782600-44785600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr21:44782600-44785800	Enhancers	Fetal Brain Female	brain
9	chr21:44782600-44787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr21:44782600-44787000	Weak transcription	Brain Substantia Nigra	brain
11	chr21:44782600-44787800	Enhancers	Fetal Muscle Leg	muscle
12	chr21:44782600-44788800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr21:44782600-44790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:44782800-44785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr21:44782800-44787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr21:44782800-44788600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr21:44782800-44790000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr21:44783000-44786000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr21:44783000-44788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr21:44783000-44789000	Weak transcription	HMEC	breast
21	chr21:44783000-44790000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr21:44783200-44785600	Weak transcription	Brain Angular Gyrus	brain
23	chr21:44783200-44786800	Weak transcription	Fetal Lung	lung
24	chr21:44783400-44786200	Enhancers	Fetal Intestine Small	intestine
25	chr21:44783400-44788600	Weak transcription	Esophagus	oesophagus
26	chr21:44783600-44785800	Bivalent Enhancer	HepG2	liver
27	chr21:44783800-44788200	Weak transcription	GM12878-XiMat	blood
28	chr21:44784200-44788200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr21:44784200-44788800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr21:44784400-44786200	Enhancers	Fetal Heart	heart
31	chr21:44784600-44786200	Enhancers	Right Ventricle	heart
32	chr21:44784800-44785600	Enhancers	Fetal Intestine Large	intestine
33	chr21:44784800-44786200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr21:44784800-44789000	Enhancers	Brain Germinal Matrix	brain
35	chr21:44784800-44791400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr21:44785000-44785800	Enhancers	Right Atrium	heart
37	chr21:44785000-44789600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr21:44785200-44786200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr21:44785200-44786200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr21:44785200-44786800	Enhancers	Left Ventricle	heart
41	chr21:44785200-44791000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr21:44785400-44785800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:44785400-44785800	Enhancers	Colonic Mucosa	Colon
44	chr21:44785400-44786000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr21:44785400-44786200	Enhancers	Ovary	ovary
46	chr21:44785400-44786400	Enhancers	Brain Hippocampus Middle	brain
47	chr21:44785400-44788600	Enhancers	Brain Anterior Caudate	brain
48	chr21:44785400-44788600	Weak transcription	Gastric	stomach
49	chr21:44785400-44789400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links