Variant report

Variant	rs6050422
Chromosome Location	chr20:25177920-25177921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:
2	chr20:25174902..25179249-chr20:25225017..25231959,9	MCF-7	breast:
3	chr20:25176590..25179411-chr20:25196913..25199010,2	MCF-7	breast:
4	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
5	chr20:25177563..25180784-chr20:25185797..25188604,4	MCF-7	breast:
6	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
7	chr20:25176534..25179250-chr20:25179296..25181376,2	MCF-7	breast:
8	chr20:25177243..25179011-chr20:25246862..25248615,2	K562	blood:
9	chr20:25175979..25179968-chr20:25200206..25203711,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1007707	0.92[CEU][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs1007708	0.83[AMR][1000 genomes]
rs11087505	0.83[AMR][1000 genomes]
rs11698185	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1473695	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes]
rs2268879	0.88[CEU][hapmap];0.89[CHD][hapmap]
rs6037057	0.86[AMR][1000 genomes]
rs6037059	0.82[AMR][1000 genomes]
rs6050425	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050426	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050427	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs6050429	0.85[AMR][1000 genomes]
rs6050431	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6050432	0.83[AMR][1000 genomes]
rs6050439	0.83[AMR][1000 genomes]
rs6050442	0.81[AMR][1000 genomes]
rs6050445	0.82[AMR][1000 genomes]
rs6083776	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs6138537	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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
18	nsv3340	chr20:25160137-25190540	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6050422	ABHD12	cis	Frontal Cortex	GTEx
rs6050422	C20orf22	cis	multi-tissue	Pritchard
rs6050422	ENTPD6	cis	parietal	SCAN
rs6050422	ABHD12	cis	Brain Pons	GTEx
rs6050422	CSTL1	cis	cerebellum	SCAN
rs6050422	ABHD12	cis	lymphoblastoid	seeQTL
rs6050422	HDHD4	cis	multi-tissue	Pritchard
rs6050422	PYGB	cis	cerebellum	SCAN
rs6050422	ABHD12	cis	brain	seeQTL
rs6050422	NINL	cis	cerebellum	SCAN
rs6050422	ABHD12	cis	Cerebellum	GTEx
rs6050422	NINL	cis	parietal	SCAN
rs6050422	PYGB	cis	multi-tissue	Pritchard
rs6050422	ABHD12	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25175800-25178000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr20:25175800-25178200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr20:25176200-25178000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr20:25176600-25178000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr20:25176600-25178000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr20:25176600-25178000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:25176600-25178200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr20:25176600-25178200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr20:25176600-25178200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr20:25176800-25178000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr20:25176800-25178000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr20:25176800-25178000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr20:25176800-25178000	Flanking Active TSS	Fetal Thymus	thymus
14	chr20:25176800-25178000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr20:25176800-25178200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr20:25177000-25178000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr20:25177000-25178000	Flanking Active TSS	Fetal Brain Male	brain
18	chr20:25177000-25178000	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr20:25177000-25178200	Flanking Active TSS	HMEC	breast
20	chr20:25177000-25178400	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr20:25177000-25178400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr20:25177000-25178400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr20:25177000-25178400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr20:25177000-25178400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr20:25177000-25178400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:25177000-25178600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr20:25177000-25178600	Flanking Active TSS	GM12878-XiMat	blood
28	chr20:25177000-25178800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:25177200-25178000	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr20:25177200-25178000	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr20:25177200-25178000	Flanking Active TSS	Hela-S3	cervix
32	chr20:25177200-25178200	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr20:25177200-25178400	Enhancers	Small Intestine	intestine
34	chr20:25177200-25178600	Flanking Active TSS	Right Ventricle	heart
35	chr20:25177200-25178600	Enhancers	Spleen	Spleen
36	chr20:25177400-25178000	Enhancers	Fetal Lung	lung
37	chr20:25177400-25178000	Flanking Active TSS	A549	lung
38	chr20:25177400-25178000	Flanking Active TSS	HepG2	liver
39	chr20:25177400-25178200	Flanking Active TSS	Pancreas	Pancrea
40	chr20:25177400-25178200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr20:25177400-25178400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr20:25177400-25178400	Flanking Active TSS	Colonic Mucosa	Colon
43	chr20:25177400-25178400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr20:25177400-25178600	Enhancers	Liver	Liver
45	chr20:25177400-25179400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr20:25177400-25179400	Weak transcription	HSMMtube	muscle
47	chr20:25177600-25178000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:25177600-25178000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:25177600-25178000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
50	chr20:25177600-25178000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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