Variant report

Variant	rs6115154
Chromosome Location	chr20:25327526-25327527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25326249..25327757-chr20:25332487..25334812,2	MCF-7	breast:
2	chr20:25326532..25328200-chr20:25370119..25372568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs56059261	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56251619	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56291736	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6107016	0.85[EUR][1000 genomes]
rs6107023	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6107024	0.92[EUR][1000 genomes]
rs6107039	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6115115	0.85[EUR][1000 genomes]
rs6115130	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6115142	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6115145	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6115151	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115177	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6115178	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6115187	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66638809	0.92[EUR][1000 genomes]
rs73101732	0.85[EUR][1000 genomes]
rs73107411	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73107474	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8119343	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6115154	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25305000-25331800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr20:25305400-25335000	Weak transcription	Primary B cells from cord blood	blood
4	chr20:25306200-25335800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr20:25309600-25333200	Weak transcription	NHLF	lung
6	chr20:25310200-25332000	Weak transcription	Colon Smooth Muscle	Colon
7	chr20:25310400-25334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:25310600-25334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:25317000-25327600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:25317600-25335600	Weak transcription	Small Intestine	intestine
11	chr20:25319200-25334200	Weak transcription	Right Ventricle	heart
12	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:25319400-25337000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr20:25319600-25328600	Weak transcription	Fetal Stomach	stomach
15	chr20:25319600-25331400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr20:25319600-25334600	Weak transcription	Fetal Brain Female	brain
17	chr20:25319600-25337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:25319800-25334400	Weak transcription	Fetal Kidney	kidney
19	chr20:25320000-25336800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr20:25321200-25331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:25321200-25334200	Weak transcription	Ovary	ovary
22	chr20:25321400-25331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:25322200-25334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr20:25322400-25336600	Weak transcription	Fetal Heart	heart
25	chr20:25322800-25331000	Weak transcription	Fetal Intestine Small	intestine
26	chr20:25323400-25333400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:25323600-25333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr20:25323600-25333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr20:25324200-25331000	Weak transcription	Pancreas	Pancrea
30	chr20:25324200-25333400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr20:25324200-25337200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr20:25324400-25334200	Weak transcription	Left Ventricle	heart
33	chr20:25325400-25331400	Weak transcription	Brain Angular Gyrus	brain
34	chr20:25325400-25334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr20:25325400-25334200	Weak transcription	GM12878-XiMat	blood
36	chr20:25325400-25336600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25325600-25331400	Weak transcription	Brain Hippocampus Middle	brain
38	chr20:25325600-25333600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr20:25325600-25334200	Weak transcription	A549	lung
40	chr20:25325600-25336600	Weak transcription	Dnd41	blood
41	chr20:25326800-25327800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr20:25327000-25327800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr20:25327000-25328000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr20:25327000-25328800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr20:25327200-25327800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr20:25327200-25327800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood

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