Variant report

Variant	rs11699401
Chromosome Location	chr20:25180114-25180115
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25178198..25180990-chr20:25188876..25192724,4	MCF-7	breast:
2	chr20:25175993..25177808-chr20:25179457..25181859,3	K562	blood:
3	chr20:25177563..25180784-chr20:25185797..25188604,4	MCF-7	breast:
4	chr20:25176534..25179250-chr20:25179296..25181376,2	MCF-7	breast:

Variant related genes	Relation type
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	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11699392	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2076559	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076560	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2076561	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2268880	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2387733	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3787075	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4456769	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55829781	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55927253	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56151505	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66536580	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66653710	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67459375	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67555242	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68008460	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8115509	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8122855	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[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
rs11699401	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs11699401	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25177600-25180800	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr20:25177600-25190400	Weak transcription	HUVEC	blood vessel
3	chr20:25177800-25180200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:25177800-25180200	Enhancers	Colon Smooth Muscle	Colon
5	chr20:25177800-25184400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:25177800-25185200	Weak transcription	Placenta	Placenta
7	chr20:25177800-25191600	Weak transcription	NH-A	brain
8	chr20:25178000-25180200	Enhancers	Fetal Thymus	thymus
9	chr20:25178000-25181000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr20:25178000-25184000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
12	chr20:25178200-25180400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr20:25178200-25180600	Genic enhancers	HepG2	liver
14	chr20:25178200-25184200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr20:25178200-25185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr20:25178200-25185800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
20	chr20:25178400-25180200	Genic enhancers	A549	lung
21	chr20:25178400-25180200	Weak transcription	NHLF	lung
22	chr20:25178400-25180600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr20:25178400-25180800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr20:25178400-25180800	Enhancers	Colonic Mucosa	Colon
25	chr20:25178400-25180800	Enhancers	Fetal Brain Female	brain
26	chr20:25178400-25181200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr20:25178400-25183400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr20:25178400-25183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr20:25178400-25184000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:25178400-25184000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:25178400-25184400	Weak transcription	Osteobl	bone
32	chr20:25178400-25184800	Weak transcription	Stomach Mucosa	stomach
33	chr20:25178400-25190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
35	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
36	chr20:25178600-25180200	Enhancers	Right Ventricle	heart
37	chr20:25178600-25180800	Enhancers	Brain Anterior Caudate	brain
38	chr20:25178600-25180800	Enhancers	Fetal Brain Male	brain
39	chr20:25178600-25181400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:25178600-25181600	Enhancers	Fetal Heart	heart
41	chr20:25178600-25183400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr20:25178600-25183600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr20:25178600-25184000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:25178600-25185200	Weak transcription	Fetal Intestine Large	intestine
45	chr20:25178600-25185800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr20:25178600-25185800	Weak transcription	Spleen	Spleen
47	chr20:25178600-25186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr20:25178600-25187400	Weak transcription	Liver	Liver
49	chr20:25178600-25190400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr20:25178600-25190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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