Variant report

Variant	rs6138584
Chromosome Location	chr20:25463148-25463149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25462596..25464466-chr20:25477326..25479004,2	MCF-7	breast:
2	chr20:25277010..25279912-chr20:25462998..25464763,2	K562	blood:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2072975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072977	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235605	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2235606	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2235607	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2261177	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2263205	0.88[AMR][1000 genomes]
rs2294583	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2482933	0.86[AMR][1000 genomes]
rs2482934	0.86[AMR][1000 genomes]
rs2482947	0.88[AMR][1000 genomes]
rs2500395	0.81[AMR][1000 genomes]
rs2500403	0.88[AMR][1000 genomes]
rs2500441	0.88[AMR][1000 genomes]
rs2500442	0.81[AMR][1000 genomes]
rs59046052	0.88[AMR][1000 genomes]
rs6050603	0.83[AMR][1000 genomes]
rs6132842	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6132851	0.88[AMR][1000 genomes]
rs6138569	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138573	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138576	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6138580	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138595	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138598	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138599	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138601	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138604	0.92[AMR][1000 genomes]
rs6138611	0.86[AMR][1000 genomes]
rs6138616	0.88[AMR][1000 genomes]
rs6138622	0.88[AMR][1000 genomes]
rs6138623	0.88[AMR][1000 genomes]
rs6138625	0.83[AMR][1000 genomes]
rs6138631	0.83[AMR][1000 genomes]
rs6138633	0.85[AMR][1000 genomes]
rs723774	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs878176	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
15	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
17	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6138584	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6138584	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138584	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138584	PYGB	cis	Whole Blood	GTEx
rs6138584	GINS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
2	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
4	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:25435800-25465600	Weak transcription	NH-A	brain
6	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:25438800-25472600	Strong transcription	HepG2	liver
9	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
10	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
11	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
13	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
14	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:25448800-25464600	Weak transcription	HUVEC	blood vessel
17	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr20:25451200-25474000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:25451400-25468400	Weak transcription	Osteobl	bone
20	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr20:25451600-25470000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr20:25451800-25468000	Weak transcription	HSMMtube	muscle
23	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
24	chr20:25453600-25467200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:25455200-25465200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr20:25456200-25466200	Strong transcription	Fetal Intestine Small	intestine
27	chr20:25456400-25470800	Strong transcription	Fetal Lung	lung
28	chr20:25456400-25472600	Strong transcription	Fetal Intestine Large	intestine
29	chr20:25456600-25463200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:25456600-25469600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr20:25456800-25463200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr20:25456800-25464800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr20:25457000-25471600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr20:25457600-25474000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr20:25457800-25489000	Weak transcription	Placenta	Placenta
36	chr20:25459400-25464000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25459600-25464200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr20:25459800-25489800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:25460200-25464200	Weak transcription	Fetal Brain Male	brain
40	chr20:25460200-25464400	Weak transcription	Brain Angular Gyrus	brain
41	chr20:25460200-25469600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:25460600-25464200	Weak transcription	HMEC	breast
43	chr20:25461200-25468000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:25461400-25465200	Weak transcription	Fetal Kidney	kidney
45	chr20:25461600-25465600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr20:25461600-25466800	Weak transcription	Fetal Heart	heart
47	chr20:25461600-25468200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:25461800-25469600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr20:25462600-25464000	Genic enhancers	Dnd41	blood
50	chr20:25462600-25464200	Weak transcription	A549	lung

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