Variant report

Variant	rs2500434
Chromosome Location	chr20:25305250-25305251
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs2039400	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258671	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	1.00[AMR][1000 genomes]
rs2474770	1.00[AMR][1000 genomes]
rs2474772	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2474775	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2474776	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482920	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs423248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs429120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs430595	0.82[YRI][hapmap]
rs432403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs518336	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs6037089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs73904036	1.00[AMR][1000 genomes]
rs73904038	1.00[AMR][1000 genomes]
rs73904039	1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
10	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
11	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
12	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
13	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
14	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25278800-25305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:25292000-25310000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25292000-25325200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr20:25292000-25327400	Weak transcription	Aorta	Aorta
5	chr20:25292200-25305600	Weak transcription	Hela-S3	cervix
6	chr20:25292200-25309600	Weak transcription	Psoas Muscle	Psoas
7	chr20:25292200-25316600	Weak transcription	NHEK	skin
8	chr20:25292400-25308400	Weak transcription	HSMMtube	muscle
9	chr20:25292400-25308600	Weak transcription	HSMM	muscle
10	chr20:25292400-25311200	Weak transcription	K562	blood
11	chr20:25292400-25325200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr20:25292600-25309000	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
14	chr20:25294400-25306400	Strong transcription	Dnd41	blood
15	chr20:25296400-25306000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:25296600-25310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr20:25296800-25305400	Weak transcription	HMEC	breast
18	chr20:25296800-25308200	Weak transcription	NH-A	brain
19	chr20:25296800-25308800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr20:25296800-25316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:25297800-25317800	Weak transcription	Fetal Brain Female	brain
22	chr20:25298000-25306000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr20:25299800-25306400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr20:25300000-25306200	Strong transcription	Thymus	Thymus
25	chr20:25301000-25306800	Weak transcription	Fetal Lung	lung
26	chr20:25301600-25305800	Weak transcription	Right Atrium	heart
27	chr20:25301600-25308400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:25301600-25309000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr20:25302200-25317200	Weak transcription	Esophagus	oesophagus
30	chr20:25302400-25307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:25302600-25309400	Weak transcription	Stomach Mucosa	stomach
32	chr20:25302800-25305600	Weak transcription	Fetal Thymus	thymus
33	chr20:25302800-25305800	Strong transcription	Fetal Stomach	stomach
34	chr20:25302800-25306000	Weak transcription	Brain Anterior Caudate	brain
35	chr20:25302800-25308400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr20:25302800-25309000	Weak transcription	Brain Angular Gyrus	brain
37	chr20:25302800-25309600	Weak transcription	Ovary	ovary
38	chr20:25302800-25324400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:25303000-25305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr20:25303000-25308400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr20:25303400-25310200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr20:25304000-25305400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr20:25304000-25307200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr20:25304000-25309800	Weak transcription	Brain Germinal Matrix	brain
45	chr20:25304000-25310000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr20:25304000-25324800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr20:25304200-25305400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr20:25304200-25305400	Enhancers	Duodenum Mucosa	Duodenum
49	chr20:25304200-25305400	Genic enhancers	Fetal Intestine Large	intestine
50	chr20:25304200-25306000	Enhancers	Placenta	Placenta

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