Variant report

Variant	rs2268880
Chromosome Location	chr20:25179107-25179108
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:
2	chr20:25178198..25180990-chr20:25188876..25192724,4	MCF-7	breast:
3	chr20:25174902..25179249-chr20:25225017..25231959,9	MCF-7	breast:
4	chr20:25176590..25179411-chr20:25196913..25199010,2	MCF-7	breast:
5	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
6	chr20:25177563..25180784-chr20:25185797..25188604,4	MCF-7	breast:
7	chr20:25176534..25179250-chr20:25179296..25181376,2	MCF-7	breast:
8	chr20:25175979..25179968-chr20:25200206..25203711,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11699328	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11699392	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11699401	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076559	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076560	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076561	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2387733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787075	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456769	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55829781	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55927253	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56151505	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66536580	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66653710	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67459375	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67555242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68008460	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8115509	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8122855	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv3340	chr20:25160137-25190540	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2268880	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2268880	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25177400-25179400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:25177400-25179400	Weak transcription	HSMMtube	muscle
3	chr20:25177600-25179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:25177600-25179600	Weak transcription	NHDF-Ad	bronchial
5	chr20:25177600-25180800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr20:25177600-25190400	Weak transcription	HUVEC	blood vessel
7	chr20:25177800-25179400	Weak transcription	HSMM	muscle
8	chr20:25177800-25179600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:25177800-25180200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:25177800-25180200	Enhancers	Colon Smooth Muscle	Colon
11	chr20:25177800-25184400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr20:25177800-25185200	Weak transcription	Placenta	Placenta
13	chr20:25177800-25191600	Weak transcription	NH-A	brain
14	chr20:25178000-25179400	Weak transcription	Psoas Muscle	Psoas
15	chr20:25178000-25179400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr20:25178000-25179600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:25178000-25179600	Weak transcription	Esophagus	oesophagus
18	chr20:25178000-25179800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:25178000-25180000	Enhancers	Brain Germinal Matrix	brain
20	chr20:25178000-25180200	Enhancers	Fetal Thymus	thymus
21	chr20:25178000-25181000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr20:25178000-25184000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
24	chr20:25178200-25179200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:25178200-25179200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr20:25178200-25179400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr20:25178200-25179400	Weak transcription	Ovary	ovary
28	chr20:25178200-25179600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr20:25178200-25179600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:25178200-25179600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:25178200-25179800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr20:25178200-25180000	Enhancers	Pancreas	Pancrea
33	chr20:25178200-25180000	Weak transcription	K562	blood
34	chr20:25178200-25180400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr20:25178200-25180600	Genic enhancers	HepG2	liver
36	chr20:25178200-25184200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr20:25178200-25185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr20:25178200-25185800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
42	chr20:25178400-25179200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:25178400-25179200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr20:25178400-25179200	Weak transcription	Fetal Stomach	stomach
45	chr20:25178400-25179200	Weak transcription	Gastric	stomach
46	chr20:25178400-25179200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr20:25178400-25179400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:25178400-25179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr20:25178400-25179400	Weak transcription	Fetal Muscle Leg	muscle
50	chr20:25178400-25179400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links