Variant report

Variant	rs6050464
Chromosome Location	chr20:25209299-25209300
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25208993-25209379	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25208292..25210129-chr20:25227027..25228548,2	MCF-7	breast:
2	chr20:25209268..25211969-chr20:25218955..25220793,2	MCF-7	breast:
3	chr20:25209269..25211589-chr20:25226481..25229322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268302	TF binding region
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1044573	0.94[EUR][1000 genomes]
rs11699953	0.90[EUR][1000 genomes]
rs1555330	0.90[EUR][1000 genomes]
rs3746337	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6037062	0.80[EUR][1000 genomes]
rs6050463	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6107015	0.82[EUR][1000 genomes]
rs6107017	0.90[EUR][1000 genomes]
rs6115093	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115094	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132819	0.82[EUR][1000 genomes]
rs6132821	0.90[EUR][1000 genomes]
rs6132822	0.86[EUR][1000 genomes]
rs6132824	0.90[EUR][1000 genomes]
rs6138545	0.80[EUR][1000 genomes]
rs6138546	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6138555	0.89[EUR][1000 genomes]
rs7453	0.83[EUR][1000 genomes]
rs8115257	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8184820	0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6050464	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6050464	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6050464	PYGB	cis	Whole Blood	GTEx
rs6050464	PYGB	cis	multi-tissue	Pritchard
rs6050464	ABHD12	cis	Nerve Tibial	GTEx
rs6050464	ABHD12	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
4	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
5	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
6	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr20:25202200-25209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr20:25204800-25210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr20:25206200-25211400	Enhancers	Right Atrium	heart
17	chr20:25206400-25210000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr20:25206600-25214000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:25206800-25212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr20:25207000-25210200	Weak transcription	Fetal Brain Female	brain
22	chr20:25207200-25209400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr20:25207200-25210800	Enhancers	Right Ventricle	heart
24	chr20:25207200-25212600	Weak transcription	Brain Germinal Matrix	brain
25	chr20:25207200-25213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr20:25207200-25213800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr20:25207400-25209400	Enhancers	Fetal Muscle Trunk	muscle
28	chr20:25207400-25211000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr20:25207400-25213200	Weak transcription	Fetal Thymus	thymus
30	chr20:25207800-25210600	Weak transcription	Aorta	Aorta
31	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
32	chr20:25207800-25218200	Weak transcription	Dnd41	blood
33	chr20:25208000-25210600	Weak transcription	Fetal Stomach	stomach
34	chr20:25208000-25212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:25208000-25212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr20:25208400-25209400	Enhancers	Stomach Smooth Muscle	stomach
37	chr20:25208400-25210000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr20:25208400-25210000	Weak transcription	Brain Hippocampus Middle	brain
39	chr20:25208400-25210000	Weak transcription	Stomach Mucosa	stomach
40	chr20:25208400-25210200	Weak transcription	Brain Anterior Caudate	brain
41	chr20:25208400-25210400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr20:25208400-25210600	Weak transcription	Thymus	Thymus
43	chr20:25208400-25212200	Weak transcription	Primary T cells from cord blood	blood
44	chr20:25208400-25213400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr20:25208400-25213600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr20:25208400-25214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr20:25208400-25214000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr20:25208400-25214000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr20:25208400-25214000	Weak transcription	Placenta	Placenta
50	chr20:25208400-25214200	Weak transcription	Brain Substantia Nigra	brain

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