Variant report

Variant	rs2179638
Chromosome Location	chr20:25205031-25205032
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25204548-25206645	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:25204482-25205329	A549	lung:	n/a	n/a
3	POLR2A	chr20:25204777-25205205	GM12878	blood:	n/a	n/a
4	EBF1	chr20:25204923-25205081	GM12878	blood:	n/a	chr20:25205040-25205051
5	POLR2A	chr20:25203686-25205925	SK-N-MC	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25200007..25207026-chr20:25227086..25230373,11	MCF-7	breast:
2	chr20:25204544..25206460-chr20:25206464..25208599,2	MCF-7	breast:
3	chr20:25204037..25205721-chr20:25227160..25229400,2	K562	blood:
4	chr20:25204221..25206637-chr20:25227058..25229400,2	K562	blood:
5	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
6	chr20:25202506..25206898-chr20:25226343..25231297,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENTPD6	TF binding region
ENSG00000100994	Chromatin interaction
ENSG00000268302	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11087508	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2227891	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2228976	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2236180	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2254046	0.90[EUR][1000 genomes]
rs2257370	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs2258052	0.82[EUR][1000 genomes]
rs2258053	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2263205	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs2281559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2424701	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2424705	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424707	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424709	0.82[EUR][1000 genomes]
rs2482933	0.81[EUR][1000 genomes]
rs2482934	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs2500403	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap]
rs2500442	0.87[EUR][1000 genomes]
rs3787078	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3787081	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs6050438	0.81[CHB][hapmap]
rs6138539	0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs753009	0.89[EUR][1000 genomes]
rs8116542	0.80[AMR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2179638	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs2179638	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2179638	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2179638	PYGB	cis	Whole Blood	GTEx
rs2179638	PYGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr20:25190400-25205200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:25190400-25207200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr20:25190400-25207200	Strong transcription	Fetal Stomach	stomach
7	chr20:25190400-25207200	Strong transcription	Ovary	ovary
8	chr20:25190600-25207000	Strong transcription	Fetal Brain Female	brain
9	chr20:25190600-25207200	Strong transcription	Brain Germinal Matrix	brain
10	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
11	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
13	chr20:25197200-25208000	Weak transcription	Primary B cells from cord blood	blood
14	chr20:25197400-25207400	Weak transcription	Fetal Brain Male	brain
15	chr20:25197400-25207400	Weak transcription	NHDF-Ad	bronchial
16	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
17	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
18	chr20:25198800-25207200	Genic enhancers	Right Ventricle	heart
19	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:25199200-25207400	Weak transcription	Psoas Muscle	Psoas
21	chr20:25199200-25208600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr20:25199600-25206000	Weak transcription	Aorta	Aorta
26	chr20:25200200-25207400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr20:25201200-25207400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr20:25201600-25208200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr20:25201800-25205600	Strong transcription	Pancreas	Pancrea
30	chr20:25201800-25205800	Weak transcription	Brain Substantia Nigra	brain
31	chr20:25201800-25207000	Strong transcription	Lung	lung
32	chr20:25202000-25205200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr20:25202000-25207200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr20:25202200-25207400	Weak transcription	Colon Smooth Muscle	Colon
35	chr20:25202200-25209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr20:25202400-25206000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr20:25202400-25206400	Weak transcription	Liver	Liver
38	chr20:25202600-25205400	Enhancers	NH-A	brain
39	chr20:25202800-25205200	Enhancers	HepG2	liver
40	chr20:25202800-25206000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:25202800-25206000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr20:25202800-25206200	Enhancers	HMEC	breast
43	chr20:25202800-25207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:25203000-25205200	Genic enhancers	NHLF	lung
45	chr20:25203000-25205400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:25203200-25207600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:25203400-25206000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr20:25203400-25206200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr20:25203600-25205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr20:25203600-25206200	Weak transcription	Right Atrium	heart

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