Variant report

Variant	rs8119343
Chromosome Location	chr20:25220536-25220537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25218111..25220827-chr20:25369556..25371592,2	MCF-7	breast:
2	chr20:25209268..25211969-chr20:25218955..25220793,2	MCF-7	breast:
3	chr20:25180225..25182029-chr20:25219353..25221557,2	MCF-7	breast:
4	chr20:25212487..25223003-chr20:25225155..25231821,24	MCF-7	breast:
5	chr20:25210927..25216331-chr20:25216727..25222043,13	MCF-7	breast:
6	chr20:25219110..25221790-chr20:25233245..25235251,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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];0.83[EUR][1000 genomes]
rs6050456	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6107016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6107023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6107024	0.84[EUR][1000 genomes]
rs6115092	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6115097	0.87[EUR][1000 genomes]
rs6115115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6115130	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6115142	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6115145	0.85[EUR][1000 genomes]
rs6115151	0.82[EUR][1000 genomes]
rs6115154	0.82[EUR][1000 genomes]
rs6115177	1.00[CEU][hapmap]
rs6115178	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs66638809	0.84[EUR][1000 genomes]
rs73101732	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73107411	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8119343	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr20:25213200-25221800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:25213400-25222200	Enhancers	HMEC	breast
4	chr20:25213600-25222200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:25214200-25220800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:25214400-25223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr20:25215200-25221800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:25215400-25223200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:25215600-25221600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:25215800-25221600	Weak transcription	Fetal Kidney	kidney
11	chr20:25215800-25222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:25216000-25222800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:25217000-25220600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr20:25217200-25220800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:25217200-25220800	Enhancers	NH-A	brain
16	chr20:25217200-25221000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr20:25217400-25220800	Enhancers	K562	blood
18	chr20:25217600-25227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr20:25218800-25220800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr20:25218800-25221600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr20:25219000-25221400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr20:25219000-25222000	Enhancers	HSMM	muscle
23	chr20:25219000-25226000	Weak transcription	Colonic Mucosa	Colon
24	chr20:25219000-25227400	Weak transcription	Colon Smooth Muscle	Colon
25	chr20:25219200-25220600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:25219200-25221800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr20:25219400-25221600	Weak transcription	Fetal Heart	heart
28	chr20:25219400-25221800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:25219400-25222000	Enhancers	NHEK	skin
30	chr20:25219400-25226800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr20:25219400-25226800	Weak transcription	Right Ventricle	heart
32	chr20:25219400-25227600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr20:25219400-25228000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr20:25219600-25220800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr20:25219600-25222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:25219600-25227000	Weak transcription	NHDF-Ad	bronchial
37	chr20:25219800-25221600	Weak transcription	HSMMtube	muscle
38	chr20:25219800-25227400	Weak transcription	NHLF	lung
39	chr20:25220000-25221600	Weak transcription	Osteobl	bone
40	chr20:25220200-25221400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:25220200-25221600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr20:25220200-25222200	Enhancers	A549	lung
43	chr20:25220200-25227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:25220400-25220600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr20:25220400-25221600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr20:25220400-25227400	Weak transcription	Esophagus	oesophagus

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