Variant report

Variant	rs60541580
Chromosome Location	chr2:20816718-20816719
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20804020..20806157-chr2:20816542..20819817,4	MCF-7	breast:
2	chr2:20801916..20805511-chr2:20814938..20817926,3	MCF-7	breast:
3	chr2:20798546..20802204-chr2:20815122..20819483,4	MCF-7	breast:
4	chr2:20812051..20815064-chr2:20816352..20817928,3	K562	blood:
5	chr2:20792170..20795116-chr2:20815831..20817825,2	MCF-7	breast:
6	chr2:20665733..20672605-chr2:20815236..20823686,12	MCF-7	breast:
7	chr2:20811207..20813551-chr2:20816352..20818633,2	K562	blood:
8	chr2:20777746..20779286-chr2:20815507..20817735,2	MCF-7	breast:
9	chr2:20644675..20653597-chr2:20811663..20819940,20	MCF-7	breast:
10	chr2:20697592..20700414-chr2:20816626..20820638,4	MCF-7	breast:
11	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
12	chr2:20787740..20790180-chr2:20814969..20816900,2	K562	blood:
13	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:
14	chr2:20666575..20668936-chr2:20816033..20817943,2	MCF-7	breast:
15	chr2:20776319..20778530-chr2:20816686..20818367,2	K562	blood:
16	chr2:20752219..20755143-chr2:20816500..20818768,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10495708	0.93[ASN][1000 genomes]
rs13027694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663045	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719114	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719159	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305459	0.81[EUR][1000 genomes]
rs34101445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34216303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35001606	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35264816	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35404888	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35527388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755927	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732150	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732158	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666441	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56905664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531249	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67364128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782402	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs744663	0.81[EUR][1000 genomes]
rs745687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870309	0.83[EUR][1000 genomes]
rs896736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active 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	10 gene(s)	inside rSNPs	diseases
6	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised 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	20 gene(s)	inside rSNPs	diseases
9	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20808400-20816800	Enhancers	Adipose Nuclei	Adipose
2	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
3	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
5	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
6	chr2:20809000-20817200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:20809600-20819200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:20810800-20819200	Weak transcription	Primary B cells from cord blood	blood
9	chr2:20810800-20819600	Enhancers	Brain Hippocampus Middle	brain
10	chr2:20811600-20820200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:20811800-20817200	Enhancers	HepG2	liver
12	chr2:20812200-20819200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:20812400-20816800	Enhancers	Spleen	Spleen
14	chr2:20812400-20817600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:20812400-20820600	Enhancers	Right Ventricle	heart
16	chr2:20812400-20820800	Enhancers	Right Atrium	heart
17	chr2:20812400-20821200	Enhancers	Left Ventricle	heart
18	chr2:20812600-20818200	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:20812600-20819200	Enhancers	Brain Angular Gyrus	brain
20	chr2:20812800-20819400	Enhancers	Fetal Lung	lung
21	chr2:20813000-20818200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:20813000-20818200	Enhancers	Fetal Intestine Large	intestine
23	chr2:20813000-20818400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:20813000-20818400	Enhancers	Lung	lung
25	chr2:20813000-20819000	Enhancers	Fetal Muscle Trunk	muscle
26	chr2:20813000-20819200	Enhancers	Esophagus	oesophagus
27	chr2:20813000-20819200	Enhancers	Psoas Muscle	Psoas
28	chr2:20813200-20816800	Weak transcription	Fetal Brain Male	brain
29	chr2:20813400-20817400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:20813600-20816800	Weak transcription	Fetal Brain Female	brain
31	chr2:20813600-20817400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:20813600-20818400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:20813600-20818600	Enhancers	Liver	Liver
34	chr2:20813600-20818600	Enhancers	Colonic Mucosa	Colon
35	chr2:20813600-20819400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr2:20813600-20819800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:20813800-20817600	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:20813800-20819200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:20813800-20819600	Enhancers	Placenta	Placenta
40	chr2:20814000-20816800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:20814000-20817800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:20814000-20818000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:20814000-20818000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:20814000-20819200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr2:20814000-20819200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:20814000-20819600	Enhancers	Pancreas	Pancrea
47	chr2:20814200-20817400	Weak transcription	HSMMtube	muscle
48	chr2:20814400-20817000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:20814400-20819200	Enhancers	Ovary	ovary
50	chr2:20814400-20819400	Genic enhancers	Fetal Intestine Small	intestine

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