Variant report

Variant	rs6138466
Chromosome Location	chr20:24997137-24997138
allele	A/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	MYC	chr20:24997136-24997153	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24996664..25000864-chr20:25037778..25041166,6	MCF-7	breast:
2	chr20:24993871..24995608-chr20:24996954..24999019,2	MCF-7	breast:

Variant related genes	Relation type
ACSS1	TF binding region
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1007881	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1056036	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11700073	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11905625	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11906373	0.81[ASN][1000 genomes]
rs1535042	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2008275	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2151462	0.81[ASN][1000 genomes]
rs2151463	0.81[ASN][1000 genomes]
rs2179732	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235847	0.94[CHD][hapmap];0.86[JPT][hapmap]
rs227616	0.81[ASN][1000 genomes]
rs227621	0.81[ASN][1000 genomes]
rs227622	0.81[ASN][1000 genomes]
rs227624	0.81[ASN][1000 genomes]
rs227625	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs227629	0.81[ASN][1000 genomes]
rs227630	0.81[ASN][1000 genomes]
rs227631	0.81[ASN][1000 genomes]
rs227632	0.81[ASN][1000 genomes]
rs227633	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs227634	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs227650	1.00[JPT][hapmap]
rs227651	0.81[ASN][1000 genomes]
rs227653	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs227658	0.81[ASN][1000 genomes]
rs2424691	0.81[ASN][1000 genomes]
rs3746330	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41315094	0.93[ASN][1000 genomes]
rs4815351	1.00[JPT][hapmap]
rs4815357	1.00[JPT][hapmap]
rs56312312	0.81[ASN][1000 genomes]
rs6037010	0.82[EUR][1000 genomes]
rs6050201	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6050249	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6050255	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6050259	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6050261	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6050263	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083699	1.00[JPT][hapmap]
rs6083709	1.00[JPT][hapmap]
rs6106984	0.81[ASN][1000 genomes]
rs6114980	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6114981	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6114984	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6114988	0.81[ASN][1000 genomes]
rs6132775	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6132777	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6132778	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132783	0.86[ASN][1000 genomes]
rs6132784	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6132785	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132789	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6138437	1.00[JPT][hapmap]
rs6138442	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138453	1.00[JPT][hapmap]
rs6138455	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138457	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138458	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6138460	0.86[ASN][1000 genomes]
rs6138461	0.82[ASN][1000 genomes]
rs6138463	0.81[ASN][1000 genomes]
rs6138464	0.93[ASN][1000 genomes]
rs6138465	0.98[ASN][1000 genomes]
rs6138473	0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6138474	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6138475	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138476	0.82[EUR][1000 genomes]
rs6707	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs7268095	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7269416	0.81[ASN][1000 genomes]
rs8125909	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8183891	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6138466	PYGB	cis	parietal	SCAN
rs6138466	NINL	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr20:24981600-25003600	Weak transcription	Fetal Heart	heart
3	chr20:24981800-24997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:24983200-25003800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr20:24983200-25005000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr20:24983200-25007800	Strong transcription	Primary T cells from cord blood	blood
7	chr20:24983200-25008200	Strong transcription	Primary B cells from cord blood	blood
8	chr20:24983800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:24984600-24997200	Strong transcription	Fetal Intestine Large	intestine
10	chr20:24985000-24997200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr20:24985000-24997600	Strong transcription	Fetal Intestine Small	intestine
12	chr20:24985000-25004400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr20:24985000-25005600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr20:24985200-25002600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr20:24985200-25003200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:24985200-25007800	Strong transcription	Fetal Muscle Leg	muscle
17	chr20:24985800-24997200	Strong transcription	Lung	lung
18	chr20:24985800-24997600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr20:24985800-25002400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr20:24985800-25004200	Strong transcription	Thymus	Thymus
21	chr20:24985800-25004400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr20:24985800-25005000	Strong transcription	Adipose Nuclei	Adipose
23	chr20:24985800-25005800	Strong transcription	Spleen	Spleen
24	chr20:24985800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:24985800-25007600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr20:24985800-25007800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:24986000-25004800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr20:24986200-25012400	Strong transcription	Dnd41	blood
29	chr20:24986400-25003800	Strong transcription	Aorta	Aorta
30	chr20:24986400-25004400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr20:24986400-25012400	Weak transcription	Fetal Brain Male	brain
32	chr20:24986600-24997400	Strong transcription	Ovary	ovary
33	chr20:24986800-24997200	Strong transcription	Brain Germinal Matrix	brain
34	chr20:24987000-24997400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:24987400-25005200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:24987600-25007800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr20:24991000-24999800	Strong transcription	Brain Substantia Nigra	brain
39	chr20:24991000-25001400	Strong transcription	Brain Anterior Caudate	brain
40	chr20:24991000-25001600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr20:24991000-25002800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr20:24991200-24998000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr20:24991800-24997600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr20:24992000-25001200	Strong transcription	Brain Hippocampus Middle	brain
45	chr20:24992200-24997600	Strong transcription	Brain Angular Gyrus	brain
46	chr20:24993400-25005200	Weak transcription	Psoas Muscle	Psoas
47	chr20:24993600-24998000	Strong transcription	Left Ventricle	heart
48	chr20:24993800-24998000	Weak transcription	Liver	Liver
49	chr20:24993800-25013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr20:24994000-24997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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