Variant report

Variant	rs6107016
Chromosome Location	chr20:25223075-25223076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2281558	1.00[YRI][hapmap]
rs3787080	1.00[YRI][hapmap]
rs56129418	0.83[AMR][1000 genomes]
rs56291736	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6050456	0.85[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6107023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6107024	0.87[EUR][1000 genomes]
rs6115092	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6115097	0.85[EUR][1000 genomes]
rs6115115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115130	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115142	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6115145	0.88[EUR][1000 genomes]
rs6115151	0.85[EUR][1000 genomes]
rs6115154	0.85[EUR][1000 genomes]
rs6115177	1.00[CEU][hapmap]
rs6115178	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs66638809	0.87[EUR][1000 genomes]
rs73101732	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73107411	0.85[EUR][1000 genomes]
rs8119343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6107016	HDHD4	cis	multi-tissue	Pritchard
rs6107016	C20orf22	cis	multi-tissue	Pritchard
rs6107016	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6107016	PYGB	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25215400-25223200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:25217600-25227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:25219000-25226000	Weak transcription	Colonic Mucosa	Colon
4	chr20:25219000-25227400	Weak transcription	Colon Smooth Muscle	Colon
5	chr20:25219400-25226800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:25219400-25226800	Weak transcription	Right Ventricle	heart
7	chr20:25219400-25227600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:25219400-25228000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr20:25219600-25227000	Weak transcription	NHDF-Ad	bronchial
10	chr20:25219800-25227400	Weak transcription	NHLF	lung
11	chr20:25220200-25227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:25220400-25227400	Weak transcription	Esophagus	oesophagus
13	chr20:25220600-25226800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:25220600-25227200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr20:25220800-25226000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:25221800-25224200	Weak transcription	Fetal Intestine Large	intestine
17	chr20:25221800-25225800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr20:25221800-25226000	Weak transcription	Fetal Heart	heart
19	chr20:25221800-25226800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr20:25221800-25226800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:25222000-25226200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr20:25222000-25226800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:25222000-25227000	Weak transcription	HSMM	muscle
24	chr20:25222000-25227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:25222000-25227400	Weak transcription	Fetal Kidney	kidney
26	chr20:25222000-25227400	Weak transcription	HSMMtube	muscle
27	chr20:25222000-25227600	Weak transcription	Fetal Lung	lung
28	chr20:25222400-25227000	Weak transcription	K562	blood
29	chr20:25222400-25227400	Weak transcription	NH-A	brain
30	chr20:25222600-25223200	Enhancers	A549	lung
31	chr20:25222600-25223400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:25222600-25224400	Enhancers	HMEC	breast
33	chr20:25222800-25223200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr20:25222800-25223200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr20:25222800-25223200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr20:25222800-25223400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25222800-25223600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr20:25222800-25223600	Enhancers	Brain Germinal Matrix	brain
39	chr20:25223000-25223200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:25223000-25223200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:25223000-25223400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr20:25223000-25223400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:25223000-25223400	Bivalent Enhancer	HepG2	liver
44	chr20:25223000-25223800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:25223000-25225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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