Variant report

Variant	rs6518284
Chromosome Location	chr21:47644428-47644429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr21:47643924-47644468	HepG2	liver:	n/a	chr21:47644189-47644200
2	CTCF	chr21:47644401-47644462	GM13976	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47627944..47629685-chr21:47643025..47644854,2	MCF-7	breast:
2	chr21:47639961..47644801-chr21:47645631..47650469,7	K562	blood:
3	chr21:47642014..47644786-chr21:47645965..47649700,6	MCF-7	breast:
4	chr21:47602541..47605503-chr21:47641795..47644690,2	K562	blood:
5	chr21:47609974..47612324-chr21:47641874..47644761,2	MCF-7	breast:
6	chr21:47636612..47639607-chr21:47641747..47644715,2	K562	blood:
7	chr21:47642621..47644664-chr21:47647031..47649590,2	MCF-7	breast:
8	chr21:47634084..47637730-chr21:47641700..47644569,3	MCF-7	breast:

No data

Variant related genes	Relation type
MCM3AP-AS1	TF binding region
ENSG00000215424	Chromatin interaction
ENSG00000160285	Chromatin interaction
ENSG00000228404	Chromatin interaction
ENSG00000160284	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11089053	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11701729	0.91[ASN][1000 genomes]
rs11909228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11909555	0.89[ASN][1000 genomes]
rs2075906	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2156116	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254522	0.90[ASN][1000 genomes]
rs2277824	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2839147	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839154	0.86[ASN][1000 genomes]
rs2839156	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839162	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2839163	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2839172	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2839177	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839182	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34105866	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818831	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6518283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518286	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7282352	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8131960	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8133857	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs914248	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976868	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9981910	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
4	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
5	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
6	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
7	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
8	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
9	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
10	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
12	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS 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 miRNA target site	95 gene(s)	inside rSNPs	n/a
13	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
14	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
15	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription 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	21 gene(s)	inside rSNPs	n/a
16	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
17	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
18	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
19	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
20	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
21	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
22	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
23	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
24	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6518284	YBEY	cis	Muscle Skeletal	GTEx
rs6518284	YBEY	cis	Artery Tibial	GTEx
rs6518284	AP001469.9	cis	Thyroid	GTEx
rs6518284	YBEY	cis	lung	GTEx
rs6518284	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs6518284	YBEY	cis	Esophagus Mucosa	GTEx
rs6518284	AP001468.1	cis	Whole Blood	GTEx
rs6518284	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs6518284	YBEY	cis	Artery Aorta	GTEx
rs6518284	YBEY	cis	Esophagus Muscularis	GTEx
rs6518284	YBEY	cis	Stomach	GTEx
rs6518284	YBEY	cis	Nerve Tibial	GTEx
rs6518284	YBEY	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
2	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
6	chr21:47612200-47645600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:47614200-47646000	Weak transcription	Fetal Brain Male	brain
8	chr21:47614200-47646200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr21:47626000-47646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr21:47626400-47646400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr21:47627800-47647000	Weak transcription	Primary B cells from cord blood	blood
12	chr21:47629200-47646200	Weak transcription	Small Intestine	intestine
13	chr21:47630400-47647000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr21:47632800-47644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:47632800-47646000	Weak transcription	NH-A	brain
16	chr21:47635000-47645400	Strong transcription	Spleen	Spleen
17	chr21:47638000-47645800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr21:47639800-47644600	Weak transcription	GM12878-XiMat	blood
19	chr21:47640600-47646200	Weak transcription	Fetal Lung	lung
20	chr21:47640800-47646000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr21:47641000-47647000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr21:47641600-47646000	Weak transcription	Colon Smooth Muscle	Colon
23	chr21:47641600-47646600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr21:47642200-47646000	Weak transcription	HSMMtube	muscle
25	chr21:47642400-47645200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:47642600-47646000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:47642600-47646200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr21:47642600-47647000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr21:47642600-47647000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr21:47642600-47647200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr21:47642800-47645400	Weak transcription	Brain Angular Gyrus	brain
32	chr21:47642800-47646000	Weak transcription	Aorta	Aorta
33	chr21:47642800-47646200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr21:47642800-47646200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr21:47642800-47646200	Weak transcription	Fetal Heart	heart
36	chr21:47642800-47646800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr21:47642800-47647000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr21:47642800-47647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr21:47643000-47644800	Strong transcription	Fetal Muscle Leg	muscle
40	chr21:47643000-47645200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr21:47643000-47645200	Weak transcription	Ovary	ovary
42	chr21:47643000-47645800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr21:47643000-47646200	Weak transcription	Colonic Mucosa	Colon
44	chr21:47643000-47646400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:47643000-47647000	Weak transcription	Thymus	Thymus
46	chr21:47643200-47645200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:47643200-47645400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr21:47643200-47646200	Weak transcription	Primary T cells from cord blood	blood
49	chr21:47643200-47646200	Weak transcription	Brain Germinal Matrix	brain
50	chr21:47643200-47646200	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links