Variant report

Variant	rs4815398
Chromosome Location	chr20:25237338-25237339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25232688..25236951-chr20:25237254..25241133,6	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1555331	1.00[CHB][hapmap]
rs2260197	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474780	0.85[CEU][hapmap]
rs4423675	0.85[CEU][hapmap]
rs4815413	0.85[CEU][hapmap]
rs6050477	0.82[CEU][hapmap]
rs6076347	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs6083824	0.85[CEU][hapmap]
rs6083841	1.00[ASN][1000 genomes]
rs6083845	0.85[CEU][hapmap]
rs6107027	0.85[CEU][hapmap]
rs6115106	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs869358	0.85[CEU][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	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4815398	PYGB	cis	Whole Blood	GTEx
rs4815398	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs4815398	HDHD4	cis	multi-tissue	Pritchard
rs4815398	PYGB	cis	cerebellum	SCAN
rs4815398	ABHD12	cis	cerebellum	SCAN
rs4815398	ABHD12	cis	lymphoblastoid	seeQTL
rs4815398	C20orf22	cis	multi-tissue	Pritchard
rs4815398	DCLRE1C	trans	multi-tissue	Pritchard
rs4815398	PYGB	cis	multi-tissue	Pritchard
rs4815398	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs4815398	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs4815398	NINL	cis	parietal	SCAN
rs4815398	NINL	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25230200-25237400	Weak transcription	Fetal Thymus	thymus
3	chr20:25230200-25239000	Weak transcription	Primary B cells from cord blood	blood
4	chr20:25230200-25239600	Enhancers	Stomach Mucosa	stomach
5	chr20:25230200-25239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:25230200-25240400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr20:25230200-25240400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:25230400-25239800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr20:25230400-25239800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:25230600-25239800	Weak transcription	Fetal Lung	lung
12	chr20:25231000-25239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr20:25231000-25239800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr20:25231000-25240400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:25231200-25239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
17	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
18	chr20:25231400-25240000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr20:25231400-25240800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr20:25231400-25249800	Weak transcription	Small Intestine	intestine
21	chr20:25232000-25237400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr20:25232000-25239400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr20:25232000-25239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr20:25232200-25238200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr20:25232400-25237600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:25232600-25238600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr20:25232600-25240000	Weak transcription	Thymus	Thymus
28	chr20:25233200-25238400	Weak transcription	K562	blood
29	chr20:25233200-25239200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:25233200-25239400	Enhancers	Primary T cells from cord blood	blood
31	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
32	chr20:25233400-25237800	Weak transcription	Fetal Muscle Leg	muscle
33	chr20:25233600-25237400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr20:25234000-25237600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:25234000-25237600	Weak transcription	GM12878-XiMat	blood
36	chr20:25234000-25239200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr20:25234000-25239200	Weak transcription	Spleen	Spleen
38	chr20:25234000-25240000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr20:25234000-25240200	Weak transcription	HSMM	muscle
40	chr20:25234400-25237600	Enhancers	Brain Angular Gyrus	brain
41	chr20:25234400-25238200	Enhancers	Brain Substantia Nigra	brain
42	chr20:25234600-25237600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:25234600-25238400	Enhancers	Adipose Nuclei	Adipose
44	chr20:25234600-25242400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr20:25235000-25237800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr20:25235000-25238200	Genic enhancers	HMEC	breast
47	chr20:25235000-25239600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr20:25235000-25243000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:25235200-25238200	Strong transcription	Fetal Intestine Small	intestine
50	chr20:25235400-25238000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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