Variant report

Variant	rs2050097
Chromosome Location	chr20:25458263-25458264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11696666	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11698953	0.85[EUR][1000 genomes]
rs11698992	0.85[EUR][1000 genomes]
rs11699872	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11700213	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11700297	0.83[EUR][1000 genomes]
rs11700338	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12480853	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs12481037	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12481409	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12625157	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12625748	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12625991	0.81[EUR][1000 genomes]
rs1888037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2072976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274890	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2281212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736720	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764694	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4815438	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6050690	0.87[CHB][hapmap]
rs6107050	0.84[ASN][1000 genomes]
rs6115202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6115227	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6115241	0.83[CHB][hapmap]
rs66807280	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68053392	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73109499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73597807	0.86[ASN][1000 genomes]
rs73597820	0.82[EUR][1000 genomes]
rs9305141	0.84[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2050097	ABHD12	cis	Temporal Cortex	GTEx
rs2050097	KIAA0980	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 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	chr20:25429800-25458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
5	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
7	chr20:25435600-25459000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr20:25435800-25465600	Weak transcription	NH-A	brain
9	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:25438800-25472600	Strong transcription	HepG2	liver
12	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
13	chr20:25442200-25460000	Weak transcription	Brain Angular Gyrus	brain
14	chr20:25443200-25459000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr20:25446000-25459600	Weak transcription	Fetal Brain Male	brain
16	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
17	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
19	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
20	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr20:25448400-25458800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr20:25448400-25459000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr20:25448800-25464600	Weak transcription	HUVEC	blood vessel
25	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:25449000-25459000	Weak transcription	Adipose Nuclei	Adipose
27	chr20:25449000-25459400	Weak transcription	Right Ventricle	heart
28	chr20:25449400-25459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:25450000-25463000	Strong transcription	Liver	Liver
30	chr20:25450800-25458800	Weak transcription	Colon Smooth Muscle	Colon
31	chr20:25451000-25461800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr20:25451000-25462000	Weak transcription	Colonic Mucosa	Colon
33	chr20:25451200-25461400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr20:25451200-25474000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:25451400-25459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr20:25451400-25460800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr20:25451400-25468400	Weak transcription	Osteobl	bone
38	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr20:25451600-25470000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr20:25451800-25458800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr20:25451800-25468000	Weak transcription	HSMMtube	muscle
42	chr20:25453200-25463000	Strong transcription	Fetal Brain Female	brain
43	chr20:25453400-25462800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
45	chr20:25453600-25467200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr20:25453800-25459000	Weak transcription	Brain Substantia Nigra	brain
47	chr20:25453800-25460600	Weak transcription	Fetal Kidney	kidney
48	chr20:25454200-25459000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:25455000-25459000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr20:25455200-25458800	Weak transcription	H9 Cell Line	embryonic stem cell

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