Variant report

Variant	rs2073077
Chromosome Location	chr20:25195913-25195914
allele	C/T
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	ZNF263	chr20:25195795-25196255	HEK293-T-REx	kidney:	n/a	n/a

Variant related genes	Relation type
ENTPD6	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11699149	0.80[CEU][hapmap]
rs1473694	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3787076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3787077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6037058	0.91[EUR][1000 genomes]
rs6050438	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6138539	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2073077	C20orf22	cis	multi-tissue	Pritchard
rs2073077	PYGB	cis	multi-tissue	Pritchard
rs2073077	NXT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
2	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
3	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:25180800-25196000	Weak transcription	Psoas Muscle	Psoas
7	chr20:25180800-25196200	Weak transcription	Fetal Brain Male	brain
8	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr20:25186400-25196000	Weak transcription	Stomach Mucosa	stomach
10	chr20:25186400-25203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr20:25188800-25197200	Weak transcription	Right Atrium	heart
12	chr20:25189000-25203000	Weak transcription	K562	blood
13	chr20:25190200-25202800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:25190200-25202800	Strong transcription	Fetal Intestine Small	intestine
15	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:25190400-25196200	Strong transcription	Brain Anterior Caudate	brain
17	chr20:25190400-25196200	Strong transcription	Left Ventricle	heart
18	chr20:25190400-25199200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr20:25190400-25199400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr20:25190400-25200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr20:25190400-25200000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:25190400-25200000	Strong transcription	Lung	lung
23	chr20:25190400-25200200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr20:25190400-25200200	Strong transcription	Fetal Muscle Leg	muscle
25	chr20:25190400-25200200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr20:25190400-25200400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr20:25190400-25200400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr20:25190400-25200400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr20:25190400-25200400	Strong transcription	A549	lung
30	chr20:25190400-25200400	Strong transcription	HepG2	liver
31	chr20:25190400-25200600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr20:25190400-25200600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr20:25190400-25200600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr20:25190400-25200800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:25190400-25201000	Strong transcription	HMEC	breast
36	chr20:25190400-25201200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr20:25190400-25201600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:25190400-25201800	Strong transcription	Adipose Nuclei	Adipose
39	chr20:25190400-25202000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:25190400-25202200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:25190400-25202200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr20:25190400-25202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr20:25190400-25202200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr20:25190400-25202400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr20:25190400-25202400	Strong transcription	Primary T cells from cord blood	blood
46	chr20:25190400-25202400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr20:25190400-25202600	Strong transcription	Spleen	Spleen
48	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr20:25190400-25202800	Strong transcription	Brain Cingulate Gyrus	brain

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