Variant report

Variant	rs6050456
Chromosome Location	chr20:25202508-25202509
allele	A/G
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	chr20:25201546-25204225	A549	lung:	n/a	n/a
2	POLR2A	chr20:25202435-25203059	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25200007..25207026-chr20:25227086..25230373,11	MCF-7	breast:
2	chr20:25175979..25179968-chr20:25200206..25203711,4	MCF-7	breast:
3	chr20:25202506..25206898-chr20:25226343..25231297,7	MCF-7	breast:

Variant related genes	Relation type
ENTPD6	TF binding region
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs6050447	0.82[GIH][hapmap]
rs6107016	0.83[EUR][1000 genomes]
rs6107023	0.85[CEU][hapmap];1.00[TSI][hapmap]
rs6115092	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6115097	0.88[EUR][1000 genomes]
rs6115115	0.83[EUR][1000 genomes]
rs6115177	0.85[CEU][hapmap]
rs6115178	0.85[CEU][hapmap];1.00[TSI][hapmap]
rs73101732	0.83[EUR][1000 genomes]
rs8119343	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6050456	C20orf22	cis	multi-tissue	Pritchard
rs6050456	HDHD4	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 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	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25186400-25203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr20:25189000-25203000	Weak transcription	K562	blood
7	chr20:25190200-25202800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:25190200-25202800	Strong transcription	Fetal Intestine Small	intestine
9	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr20:25190400-25202600	Strong transcription	Spleen	Spleen
11	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr20:25190400-25202800	Strong transcription	Brain Cingulate Gyrus	brain
14	chr20:25190400-25202800	Strong transcription	Placenta	Placenta
15	chr20:25190400-25203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:25190400-25203000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:25190400-25203000	Strong transcription	Fetal Intestine Large	intestine
18	chr20:25190400-25203000	Strong transcription	NHLF	lung
19	chr20:25190400-25203200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:25190400-25203200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:25190400-25203400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr20:25190400-25203400	Strong transcription	Dnd41	blood
23	chr20:25190400-25203600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr20:25190400-25205200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr20:25190400-25207200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr20:25190400-25207200	Strong transcription	Fetal Stomach	stomach
27	chr20:25190400-25207200	Strong transcription	Ovary	ovary
28	chr20:25190600-25207000	Strong transcription	Fetal Brain Female	brain
29	chr20:25190600-25207200	Strong transcription	Brain Germinal Matrix	brain
30	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
31	chr20:25191000-25203800	Weak transcription	HUVEC	blood vessel
32	chr20:25191600-25203200	Strong transcription	Brain Hippocampus Middle	brain
33	chr20:25191600-25204200	Strong transcription	Brain Angular Gyrus	brain
34	chr20:25192000-25202800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr20:25192000-25203600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr20:25193200-25203200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr20:25193200-25203400	Weak transcription	HSMM	muscle
38	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr20:25195200-25203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:25196600-25203200	Weak transcription	Stomach Mucosa	stomach
41	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
42	chr20:25197000-25203200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr20:25197200-25208000	Weak transcription	Primary B cells from cord blood	blood
44	chr20:25197400-25207400	Weak transcription	Fetal Brain Male	brain
45	chr20:25197400-25207400	Weak transcription	NHDF-Ad	bronchial
46	chr20:25198000-25202600	Weak transcription	NH-A	brain
47	chr20:25198000-25203200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr20:25198000-25203200	Weak transcription	HSMMtube	muscle
49	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
50	chr20:25198400-25212200	Enhancers	Fetal Heart	heart

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