Variant report

Variant	rs6138510
Chromosome Location	chr20:25128964-25128965
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr20:25128899-25128984	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr20:25128698-25129910	H1-hESC	embryonic stem cell:	n/a	chr20:25129477-25129492 chr20:25129481-25129488
3	MAX	chr20:25128686-25129838	H1-hESC	embryonic stem cell:	n/a	chr20:25129477-25129492 chr20:25129481-25129488
4	CTCF	chr20:25128900-25129170	GM12870	blood:	n/a	n/a
5	E2F6	chr20:25128558-25129941	H1-hESC	embryonic stem cell:	n/a	chr20:25129926-25129935
6	E2F6	chr20:25128727-25129152	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr20:25128858-25129899	H1-hESC	embryonic stem cell:	n/a	chr20:25129477-25129492 chr20:25129481-25129488

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSX1-1	chr20:25128593-25129426	ENSG00000230725
2	lnc-VSX1-1	chr20:25128593-25129426	XLOC_013704

Variant related genes	Relation type
ENSG00000230725	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1108810	0.98[ASN][1000 genomes]
rs1108811	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11698226	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11699149	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11699219	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11699614	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625069	0.98[ASN][1000 genomes]
rs13037201	0.94[EUR][1000 genomes]
rs13037374	0.94[EUR][1000 genomes]
rs13039237	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13041051	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043355	0.98[ASN][1000 genomes]
rs13043906	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13045280	0.99[ASN][1000 genomes]
rs13045481	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057042	0.93[ASN][1000 genomes]
rs2103715	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2235770	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892314	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34242837	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34631700	0.99[ASN][1000 genomes]
rs35047430	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35231728	0.94[EUR][1000 genomes]
rs35910458	0.91[ASN][1000 genomes]
rs36115891	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4482560	0.93[ASN][1000 genomes]
rs4815374	0.93[ASN][1000 genomes]
rs6037024	0.91[ASN][1000 genomes]
rs6037025	0.98[ASN][1000 genomes]
rs6037028	0.98[ASN][1000 genomes]
rs6037029	0.98[ASN][1000 genomes]
rs6037030	0.99[ASN][1000 genomes]
rs6037031	0.98[ASN][1000 genomes]
rs6037032	0.93[ASN][1000 genomes]
rs6037033	0.93[ASN][1000 genomes]
rs6037034	0.93[ASN][1000 genomes]
rs6037038	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6037052	0.95[EUR][1000 genomes]
rs6050341	0.99[ASN][1000 genomes]
rs6050342	0.93[ASN][1000 genomes]
rs6050345	0.93[ASN][1000 genomes]
rs6050348	0.93[ASN][1000 genomes]
rs6050351	0.99[ASN][1000 genomes]
rs6050353	0.93[ASN][1000 genomes]
rs6050359	0.93[ASN][1000 genomes]
rs6050370	0.92[ASN][1000 genomes]
rs6050390	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050397	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050400	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050403	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050408	0.91[EUR][1000 genomes]
rs6050411	0.95[EUR][1000 genomes]
rs6050412	0.95[EUR][1000 genomes]
rs6050413	0.95[EUR][1000 genomes]
rs6050421	0.87[EUR][1000 genomes]
rs6132804	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132810	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132816	0.95[EUR][1000 genomes]
rs6138492	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138493	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138496	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138504	0.98[ASN][1000 genomes]
rs6138506	0.98[ASN][1000 genomes]
rs6138511	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138519	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138520	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138521	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138528	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138531	0.95[EUR][1000 genomes]
rs6138532	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6138533	0.97[EUR][1000 genomes]
rs7261718	0.99[ASN][1000 genomes]
rs7270433	0.99[ASN][1000 genomes]
rs7270464	0.98[ASN][1000 genomes]
rs7272141	0.98[ASN][1000 genomes]
rs8115505	0.93[ASN][1000 genomes]
rs8119777	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8122274	0.93[ASN][1000 genomes]
rs910101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910102	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25127000-25129200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr20:25128200-25129200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:25128400-25129000	Bivalent Enhancer	Fetal Brain Male	brain
4	chr20:25128400-25129400	Active TSS	Fetal Brain Female	brain
5	chr20:25128600-25129200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:25128600-25130000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
7	chr20:25128600-25131600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:25128800-25129000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:25128800-25129000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr20:25128800-25129000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr20:25128800-25129000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr20:25128800-25129000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr20:25128800-25129000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:25128800-25129000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
17	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
18	chr20:25128800-25129000	Enhancers	Esophagus	oesophagus
19	chr20:25128800-25129000	Enhancers	Ovary	ovary
20	chr20:25128800-25129000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr20:25128800-25129000	Enhancers	Right Atrium	heart
22	chr20:25128800-25129000	Enhancers	Right Ventricle	heart
23	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
25	chr20:25128800-25129000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr20:25128800-25129000	Flanking Bivalent TSS/Enh	Osteobl	bone
27	chr20:25128800-25129200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:25128800-25129200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr20:25128800-25129200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr20:25128800-25129200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr20:25128800-25129200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr20:25128800-25129200	Active TSS	Brain Cingulate Gyrus	brain
33	chr20:25128800-25129200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
34	chr20:25128800-25129200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr20:25128800-25129200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr20:25128800-25129200	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr20:25128800-25129200	Bivalent Enhancer	Fetal Stomach	stomach
38	chr20:25128800-25129200	Bivalent Enhancer	Left Ventricle	heart
39	chr20:25128800-25129200	Enhancers	Pancreas	Pancrea
40	chr20:25128800-25129200	Bivalent Enhancer	Rectal Smooth Muscle	rectum
41	chr20:25128800-25129400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr20:25128800-25129400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr20:25128800-25129400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr20:25128800-25129400	Active TSS	Thymus	Thymus
45	chr20:25128800-25129600	Active TSS	Primary T cells from cord blood	blood
46	chr20:25128800-25129600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr20:25128800-25129600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr20:25128800-25129600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr20:25128800-25129800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr20:25128800-25129800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood

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