Variant report

Variant	rs6041420
Chromosome Location	chr20:1304120-1304121
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	POLR2A	chr20:1303403-1304304	HUVEC	blood vessel:	n/a	n/a
2	GATA2	chr20:1303513-1304212	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr20:1302594-1304487	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr20:1303332-1311264	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT1	chr20:1303683-1304383	Hela-S3	cervix:	n/a	chr20:1304118-1304127 chr20:1304117-1304128 chr20:1304113-1304133 chr20:1304116-1304130 chr20:1304113-1304133 chr20:1303821-1303829 chr20:1304119-1304128 chr20:1303856-1303863
6	STAT3	chr20:1303427-1304143	MCF10A-Er-Src	breast:	n/a	chr20:1304118-1304127 chr20:1304113-1304133 chr20:1304116-1304130 chr20:1304113-1304133 chr20:1304117-1304128 chr20:1303821-1303829 chr20:1304119-1304128 chr20:1303856-1303863
7	STAT3	chr20:1303426-1304156	MCF10A-Er-Src	breast:	n/a	chr20:1304118-1304127 chr20:1304113-1304133 chr20:1304116-1304130 chr20:1304113-1304133 chr20:1304117-1304128 chr20:1303821-1303829 chr20:1304119-1304128 chr20:1303856-1303863
8	POLR2A	chr20:1302125-1308990	IMR90	lung:	n/a	n/a
9	POLR2A	chr20:1303418-1304411	HUVEC	blood vessel:	n/a	n/a
10	STAT3	chr20:1304112-1304137	MCF10A-Er-Src	breast:	n/a	chr20:1304118-1304127 chr20:1304113-1304133 chr20:1304116-1304130 chr20:1304113-1304133 chr20:1304117-1304128 chr20:1304119-1304128
11	POLR2A	chr20:1303181-1304480	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr20:1303230-1304437	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr20:1303290-1308319	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1303470..1306346-chr20:1351219..1354077,2	MCF-7	breast:
2	chr20:1301486..1304353-chr20:1304834..1307376,4	MCF-7	breast:
3	chr20:1303741..1307612-chr20:1308466..1314134,7	MCF-7	breast:

Variant related genes	Relation type
SDCBP2-AS1	TF binding region
ENSG00000088832	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6109623	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv912595	chr20:1283523-1313762	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6041420	PDGFD	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1289600-1305000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:1294200-1305600	Weak transcription	Ovary	ovary
3	chr20:1294400-1304800	Weak transcription	Placenta	Placenta
4	chr20:1294600-1305200	Weak transcription	Colon Smooth Muscle	Colon
5	chr20:1294600-1305200	Weak transcription	Fetal Thymus	thymus
6	chr20:1294600-1305400	Weak transcription	Colonic Mucosa	Colon
7	chr20:1294800-1305200	Weak transcription	Dnd41	blood
8	chr20:1298600-1305000	Weak transcription	A549	lung
9	chr20:1299000-1305200	Weak transcription	GM12878-XiMat	blood
10	chr20:1299800-1304600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr20:1300400-1305200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr20:1300800-1305400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr20:1301000-1305200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr20:1301000-1305600	Weak transcription	Fetal Intestine Large	intestine
15	chr20:1301600-1305200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:1301600-1305400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr20:1301800-1305200	Weak transcription	Fetal Intestine Small	intestine
18	chr20:1302000-1304200	Enhancers	Right Atrium	heart
19	chr20:1302000-1305000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr20:1302000-1305600	Enhancers	Left Ventricle	heart
21	chr20:1302200-1305600	Enhancers	Primary hematopoietic stem cells	blood
22	chr20:1302200-1305600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr20:1302200-1305600	Enhancers	Adipose Nuclei	Adipose
24	chr20:1302400-1305200	Weak transcription	Gastric	stomach
25	chr20:1302400-1305600	Weak transcription	Esophagus	oesophagus
26	chr20:1302600-1305200	Enhancers	Stomach Smooth Muscle	stomach
27	chr20:1302800-1304600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr20:1302800-1305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr20:1302800-1305200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:1302800-1305200	Weak transcription	HepG2	liver
31	chr20:1302800-1305200	Enhancers	NHLF	lung
32	chr20:1302800-1305400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr20:1302800-1305400	Weak transcription	Liver	Liver
34	chr20:1302800-1305400	Enhancers	NHDF-Ad	bronchial
35	chr20:1302800-1305600	Weak transcription	Pancreas	Pancrea
36	chr20:1303000-1304200	Enhancers	Fetal Muscle Trunk	muscle
37	chr20:1303000-1304600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:1303000-1305400	Enhancers	NH-A	brain
39	chr20:1303200-1304200	Enhancers	Fetal Muscle Leg	muscle
40	chr20:1303200-1305200	Weak transcription	Stomach Mucosa	stomach
41	chr20:1303200-1305400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr20:1303400-1304600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr20:1303400-1305200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr20:1303400-1305400	Weak transcription	Fetal Stomach	stomach
45	chr20:1303600-1304600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr20:1303600-1305400	Enhancers	HSMM	muscle
47	chr20:1303800-1304200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:1303800-1304200	Flanking Active TSS	HUVEC	blood vessel
49	chr20:1303800-1304200	Flanking Active TSS	Osteobl	bone
50	chr20:1303800-1305200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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