Variant report

Variant	rs6037059
Chromosome Location	chr20:25191346-25191347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25176095..25177942-chr20:25190649..25192895,2	MCF-7	breast:
2	chr20:25189324..25193219-chr20:25201165..25204097,4	MCF-7	breast:
3	chr20:25178198..25180990-chr20:25188876..25192724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1007707	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1007708	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11087505	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11698185	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1473695	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6037057	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6050422	0.82[AMR][1000 genomes]
rs6050425	0.86[ASN][1000 genomes]
rs6050426	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6050427	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6050429	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6050431	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6050432	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6050439	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6050442	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6050445	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6083776	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083779	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138536	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138537	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6037059	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6037059	PYGB	cis	Whole Blood	GTEx
rs6037059	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25177800-25191600	Weak transcription	NH-A	brain
2	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
3	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
5	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
6	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
7	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr20:25180000-25191800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr20:25180000-25192200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:25180400-25192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr20:25180600-25191600	Weak transcription	HSMMtube	muscle
15	chr20:25180800-25191600	Weak transcription	NHDF-Ad	bronchial
16	chr20:25180800-25196000	Weak transcription	Psoas Muscle	Psoas
17	chr20:25180800-25196200	Weak transcription	Fetal Brain Male	brain
18	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr20:25185000-25193800	Weak transcription	Fetal Kidney	kidney
20	chr20:25185400-25191800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr20:25185600-25194000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr20:25185800-25191400	Weak transcription	Primary B cells from cord blood	blood
23	chr20:25185800-25191600	Weak transcription	Fetal Thymus	thymus
24	chr20:25185800-25191800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr20:25185800-25192200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr20:25185800-25192600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25186200-25191600	Weak transcription	Brain Substantia Nigra	brain
28	chr20:25186400-25191800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr20:25186400-25196000	Weak transcription	Stomach Mucosa	stomach
30	chr20:25186400-25203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr20:25186600-25191600	Weak transcription	Brain Angular Gyrus	brain
32	chr20:25186600-25191600	Weak transcription	Brain Hippocampus Middle	brain
33	chr20:25186600-25194000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr20:25186800-25191600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr20:25186800-25192000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:25186800-25193800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:25186800-25194000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr20:25187000-25191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr20:25187600-25192000	Weak transcription	Gastric	stomach
40	chr20:25188000-25191600	Weak transcription	GM12878-XiMat	blood
41	chr20:25188200-25192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr20:25188600-25191800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr20:25188800-25192000	Weak transcription	Pancreas	Pancrea
44	chr20:25188800-25192000	Weak transcription	Right Ventricle	heart
45	chr20:25188800-25197200	Weak transcription	Right Atrium	heart
46	chr20:25189000-25195400	Weak transcription	Fetal Heart	heart
47	chr20:25189000-25203000	Weak transcription	K562	blood
48	chr20:25190200-25202800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr20:25190200-25202800	Strong transcription	Fetal Intestine Small	intestine
50	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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