Variant report

Variant	rs6050438
Chromosome Location	chr20:25191773-25191774
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25176095..25177942-chr20:25190649..25192895,2	MCF-7	breast:
2	chr20:25189324..25193219-chr20:25201165..25204097,4	MCF-7	breast:
3	chr20:25178198..25180990-chr20:25188876..25192724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11699149	0.80[CEU][hapmap]
rs13038578	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473694	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2073077	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2179638	0.81[CHB][hapmap]
rs2228976	0.82[CHB][hapmap]
rs2257370	0.82[CHB][hapmap]
rs2281559	0.82[CHB][hapmap]
rs2424701	0.82[CHB][hapmap]
rs2482934	0.82[CHB][hapmap]
rs2500403	0.82[CHB][hapmap]
rs3787076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3787077	1.00[CEU][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6037058	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138535	0.90[ASN][1000 genomes]
rs6138539	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6050438	PYGB	cis	multi-tissue	Pritchard
rs6050438	C20orf22	cis	multi-tissue	Pritchard
rs6050438	NXT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
2	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
4	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
5	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
6	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr20:25180000-25191800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:25180000-25192200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:25180400-25192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr20:25180800-25196000	Weak transcription	Psoas Muscle	Psoas
14	chr20:25180800-25196200	Weak transcription	Fetal Brain Male	brain
15	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr20:25185000-25193800	Weak transcription	Fetal Kidney	kidney
17	chr20:25185400-25191800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr20:25185600-25194000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr20:25185800-25191800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr20:25185800-25192200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:25185800-25192600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr20:25186400-25191800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr20:25186400-25196000	Weak transcription	Stomach Mucosa	stomach
24	chr20:25186400-25203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr20:25186600-25194000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr20:25186800-25192000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr20:25186800-25193800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr20:25186800-25194000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:25187600-25192000	Weak transcription	Gastric	stomach
30	chr20:25188200-25192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:25188600-25191800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr20:25188800-25192000	Weak transcription	Pancreas	Pancrea
33	chr20:25188800-25192000	Weak transcription	Right Ventricle	heart
34	chr20:25188800-25197200	Weak transcription	Right Atrium	heart
35	chr20:25189000-25195400	Weak transcription	Fetal Heart	heart
36	chr20:25189000-25203000	Weak transcription	K562	blood
37	chr20:25190200-25202800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25190200-25202800	Strong transcription	Fetal Intestine Small	intestine
39	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr20:25190400-25193800	Strong transcription	Liver	Liver
41	chr20:25190400-25194400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr20:25190400-25194400	Strong transcription	NHEK	skin
43	chr20:25190400-25194800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr20:25190400-25196200	Strong transcription	Brain Anterior Caudate	brain
45	chr20:25190400-25196200	Strong transcription	Left Ventricle	heart
46	chr20:25190400-25199200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:25190400-25199400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr20:25190400-25200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:25190400-25200000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr20:25190400-25200000	Strong transcription	Lung	lung

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