Variant report

Variant	rs6050261
Chromosome Location	chr20:25014206-25014207
allele	C/T
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	GATA3	chr20:25013826-25014642	MCF-7	breast:	n/a	chr20:25014012-25014021
2	GATA2	chr20:25013883-25014338	SH-SY5Y	brain:	n/a	chr20:25014012-25014021
3	TCF12	chr20:25013894-25014443	SK-N-SH	brain:	n/a	chr20:25014418-25014428
4	GATA3	chr20:25013891-25014481	SK-N-SH	brain:	n/a	chr20:25014012-25014021

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25014177..25016183-chr20:25020010..25021666,2	MCF-7	breast:

Variant related genes	Relation type
ACSS1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1007881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056036	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11700073	0.86[JPT][hapmap]
rs11905625	0.86[JPT][hapmap]
rs1535042	0.86[JPT][hapmap]
rs2008275	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2179732	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs227625	0.86[JPT][hapmap]
rs227633	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs227634	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs227650	0.85[JPT][hapmap]
rs227653	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3746330	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4815351	0.86[JPT][hapmap]
rs4815357	0.86[JPT][hapmap]
rs6037010	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050201	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050249	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6050255	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050263	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083699	0.86[JPT][hapmap]
rs6083709	0.86[JPT][hapmap]
rs60849220	0.87[ASN][1000 genomes]
rs6114980	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6114981	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6114984	0.84[JPT][hapmap]
rs6132775	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6132777	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6132778	0.86[JPT][hapmap]
rs6132784	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6132785	0.83[EUR][1000 genomes]
rs6132788	0.87[ASN][1000 genomes]
rs6132789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6132790	0.91[ASN][1000 genomes]
rs6138437	0.86[JPT][hapmap]
rs6138442	0.86[JPT][hapmap]
rs6138453	0.86[JPT][hapmap]
rs6138455	0.86[JPT][hapmap]
rs6138457	0.86[JPT][hapmap]
rs6138458	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138466	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]
rs6138473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138475	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6138476	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62217173	0.84[ASN][1000 genomes]
rs62217174	0.84[ASN][1000 genomes]
rs62217175	0.84[ASN][1000 genomes]
rs6707	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7268095	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7273518	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8125909	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs8183891	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6050261	PYGB	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
5	chr20:24998600-25016600	Weak transcription	Liver	Liver
6	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr20:25004800-25016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:25007800-25014800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr20:25009200-25016600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr20:25010000-25017800	Weak transcription	NHDF-Ad	bronchial
11	chr20:25010200-25015000	Strong transcription	Primary T cells from cord blood	blood
12	chr20:25010600-25014800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr20:25011200-25014800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr20:25011200-25015200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:25011400-25014800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr20:25011400-25016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr20:25011600-25015000	Genic enhancers	Fetal Intestine Small	intestine
18	chr20:25011600-25015000	Enhancers	Left Ventricle	heart
19	chr20:25011600-25015600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr20:25011600-25016200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr20:25011600-25016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr20:25011600-25016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr20:25011600-25016800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr20:25011600-25017800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:25011600-25017800	Enhancers	Placenta	Placenta
26	chr20:25011600-25020200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:25011800-25016800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr20:25012000-25016400	Weak transcription	Thymus	Thymus
29	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
30	chr20:25012200-25015000	Enhancers	Fetal Heart	heart
31	chr20:25012200-25015200	Enhancers	Fetal Muscle Leg	muscle
32	chr20:25012400-25014600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:25012400-25014600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr20:25012400-25014600	Enhancers	Fetal Brain Male	brain
35	chr20:25012400-25014600	Enhancers	Ovary	ovary
36	chr20:25012400-25015000	Genic enhancers	Fetal Stomach	stomach
37	chr20:25012400-25015200	Enhancers	Stomach Mucosa	stomach
38	chr20:25012400-25016400	Weak transcription	Dnd41	blood
39	chr20:25012600-25014400	Enhancers	Adipose Nuclei	Adipose
40	chr20:25012600-25014600	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr20:25012600-25014600	Enhancers	Psoas Muscle	Psoas
42	chr20:25012600-25014800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr20:25012600-25014800	Enhancers	Fetal Lung	lung
44	chr20:25012600-25015000	Enhancers	Lung	lung
45	chr20:25012600-25015000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr20:25012600-25015000	Enhancers	Right Atrium	heart
47	chr20:25012600-25015200	Enhancers	Rectal Smooth Muscle	rectum
48	chr20:25012800-25014400	Enhancers	K562	blood
49	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
50	chr20:25013000-25014400	Enhancers	Fetal Thymus	thymus

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