Variant report

Variant	rs6050463
Chromosome Location	chr20:25208990-25208991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25208292..25210129-chr20:25227027..25228548,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1007708	0.80[ASN][1000 genomes]
rs1044573	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077889	0.80[ASN][1000 genomes]
rs11087505	0.80[ASN][1000 genomes]
rs1118963	1.00[ASN][1000 genomes]
rs11699953	0.89[EUR][1000 genomes]
rs1555330	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145126	0.80[ASN][1000 genomes]
rs2227890	0.80[ASN][1000 genomes]
rs2227892	0.80[ASN][1000 genomes]
rs2257233	0.80[ASN][1000 genomes]
rs2257432	0.80[ASN][1000 genomes]
rs2257461	0.80[ASN][1000 genomes]
rs2257464	0.80[ASN][1000 genomes]
rs2257705	0.80[ASN][1000 genomes]
rs2257712	0.80[ASN][1000 genomes]
rs2257808	0.80[ASN][1000 genomes]
rs2257809	0.80[ASN][1000 genomes]
rs2257982	0.80[ASN][1000 genomes]
rs2257985	0.80[ASN][1000 genomes]
rs2257991	0.80[ASN][1000 genomes]
rs2258066	0.80[ASN][1000 genomes]
rs2258135	0.80[ASN][1000 genomes]
rs2258201	0.80[ASN][1000 genomes]
rs2260997	0.90[ASN][1000 genomes]
rs2261109	0.80[ASN][1000 genomes]
rs2261115	0.80[ASN][1000 genomes]
rs2261698	0.80[ASN][1000 genomes]
rs2261720	0.80[ASN][1000 genomes]
rs2261753	0.80[ASN][1000 genomes]
rs2261784	0.80[ASN][1000 genomes]
rs2261785	0.80[ASN][1000 genomes]
rs2261790	0.80[ASN][1000 genomes]
rs2261794	0.80[ASN][1000 genomes]
rs2273473	0.84[EUR][1000 genomes]
rs2424698	0.90[ASN][1000 genomes]
rs2424700	0.80[ASN][1000 genomes]
rs2474766	1.00[ASN][1000 genomes]
rs2474769	1.00[ASN][1000 genomes]
rs2474777	0.80[ASN][1000 genomes]
rs3002702	0.80[ASN][1000 genomes]
rs33999482	0.80[ASN][1000 genomes]
rs3746337	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619688	1.00[ASN][1000 genomes]
rs6037062	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6037069	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050439	0.80[ASN][1000 genomes]
rs6050442	0.80[ASN][1000 genomes]
rs6050445	0.80[ASN][1000 genomes]
rs6050464	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050472	0.84[ASN][1000 genomes]
rs6050477	0.84[ASN][1000 genomes]
rs6050481	1.00[ASN][1000 genomes]
rs6050482	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6107015	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6107017	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107019	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115093	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115100	1.00[ASN][1000 genomes]
rs6115101	1.00[ASN][1000 genomes]
rs6115109	1.00[ASN][1000 genomes]
rs6132819	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132820	1.00[ASN][1000 genomes]
rs6132821	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132822	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132824	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138545	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138546	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138550	1.00[ASN][1000 genomes]
rs6138553	1.00[ASN][1000 genomes]
rs6138555	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138556	0.90[ASN][1000 genomes]
rs7453	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115257	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8184820	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910996	0.80[ASN][1000 genomes]
rs910997	0.80[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6050463	ABHD12	cis	multi-tissue	Pritchard
rs6050463	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6050463	PYGB	cis	multi-tissue	Pritchard
rs6050463	ABHD12	cis	Artery Tibial	GTEx
rs6050463	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6050463	PYGB	cis	Whole Blood	GTEx

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	chr20:25204400-25209200	Strong transcription	Fetal Intestine Small	intestine
14	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr20:25204800-25210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr20:25206200-25209200	Enhancers	Left Ventricle	heart
18	chr20:25206200-25211400	Enhancers	Right Atrium	heart
19	chr20:25206400-25210000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr20:25206600-25209200	Enhancers	Pancreas	Pancrea
21	chr20:25206600-25214000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr20:25206800-25209200	Enhancers	Fetal Muscle Leg	muscle
23	chr20:25206800-25212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr20:25207000-25210200	Weak transcription	Fetal Brain Female	brain
26	chr20:25207200-25209200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr20:25207200-25209400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:25207200-25210800	Enhancers	Right Ventricle	heart
29	chr20:25207200-25212600	Weak transcription	Brain Germinal Matrix	brain
30	chr20:25207200-25213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr20:25207200-25213800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr20:25207400-25209200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr20:25207400-25209400	Enhancers	Fetal Muscle Trunk	muscle
34	chr20:25207400-25211000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:25207400-25213200	Weak transcription	Fetal Thymus	thymus
36	chr20:25207800-25210600	Weak transcription	Aorta	Aorta
37	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
38	chr20:25207800-25218200	Weak transcription	Dnd41	blood
39	chr20:25208000-25210600	Weak transcription	Fetal Stomach	stomach
40	chr20:25208000-25212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:25208000-25212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr20:25208400-25209400	Enhancers	Stomach Smooth Muscle	stomach
43	chr20:25208400-25210000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr20:25208400-25210000	Weak transcription	Brain Hippocampus Middle	brain
45	chr20:25208400-25210000	Weak transcription	Stomach Mucosa	stomach
46	chr20:25208400-25210200	Weak transcription	Brain Anterior Caudate	brain
47	chr20:25208400-25210400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr20:25208400-25210600	Weak transcription	Thymus	Thymus
49	chr20:25208400-25212200	Weak transcription	Primary T cells from cord blood	blood
50	chr20:25208400-25213400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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