Variant report

Variant	rs57806058
Chromosome Location	chr20:1311863-1311864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1311640-1311965	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:1311431-1312155	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr20:1305666-1312369	K562	blood:	n/a	n/a
4	POLR2A	chr20:1310807-1312148	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr20:1311793-1311951	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr20:1311693-1311952	K562	blood:	n/a	n/a
7	POLR2A	chr20:1311565-1311958	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1311170..1313178-chr20:1375067..1377982,2	MCF-7	breast:
2	chr20:1303741..1307612-chr20:1308466..1314134,7	MCF-7	breast:
3	chr20:1310039..1313013-chr20:1319417..1322012,2	MCF-7	breast:
4	chr20:1310189..1311997-chr20:1314145..1316733,2	K562	blood:
5	chr20:1311744..1314670-chr20:1315786..1318493,2	MCF-7	breast:

No data

Variant related genes	Relation type
SDCBP2	TF binding region
ENSG00000125775	Chromatin interaction
ENSG00000203630	Chromatin interaction
ENSG00000234684	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11087048	1.00[ASN][1000 genomes]
rs13433171	1.00[ASN][1000 genomes]
rs4577347	1.00[ASN][1000 genomes]
rs4813115	1.00[ASN][1000 genomes]
rs56035174	1.00[ASN][1000 genomes]
rs59377624	1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[ASN][1000 genomes]
rs6033554	1.00[ASN][1000 genomes]
rs6033660	1.00[ASN][1000 genomes]
rs6033672	1.00[ASN][1000 genomes]
rs6033871	1.00[ASN][1000 genomes]
rs6033896	1.00[ASN][1000 genomes]
rs6041382	1.00[ASN][1000 genomes]
rs6041689	1.00[ASN][1000 genomes]
rs6041717	1.00[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[ASN][1000 genomes]
rs6042550	1.00[ASN][1000 genomes]
rs6042568	1.00[ASN][1000 genomes]
rs6042574	1.00[ASN][1000 genomes]
rs6042578	1.00[ASN][1000 genomes]
rs6104943	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6105031	1.00[ASN][1000 genomes]
rs6109437	1.00[ASN][1000 genomes]
rs6109511	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109522	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109740	1.00[ASN][1000 genomes]
rs6109784	1.00[ASN][1000 genomes]
rs6110189	1.00[ASN][1000 genomes]
rs6110193	1.00[ASN][1000 genomes]
rs62187542	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs6514337	1.00[ASN][1000 genomes]
rs6514364	1.00[ASN][1000 genomes]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73579400	0.89[AFR][1000 genomes]
rs73581208	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747611	1.00[ASN][1000 genomes]
rs8117563	1.00[ASN][1000 genomes]
rs8117744	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118276	1.00[ASN][1000 genomes]
rs8119259	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958839	1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1307000-1312000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr20:1307000-1314400	Enhancers	Left Ventricle	heart
3	chr20:1307200-1312000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:1307200-1312800	Enhancers	Right Ventricle	heart
5	chr20:1307200-1313200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:1307200-1315400	Weak transcription	Aorta	Aorta
7	chr20:1307400-1312000	Enhancers	Brain Anterior Caudate	brain
8	chr20:1307400-1312600	Weak transcription	Primary B cells from cord blood	blood
9	chr20:1307400-1319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:1307600-1312000	Weak transcription	Fetal Lung	lung
11	chr20:1307600-1314400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr20:1307600-1315200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr20:1307600-1315200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr20:1307600-1315800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:1307600-1327200	Weak transcription	Fetal Brain Female	brain
16	chr20:1307600-1340400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:1307800-1312000	Enhancers	Adipose Nuclei	Adipose
18	chr20:1307800-1315200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:1307800-1316200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr20:1307800-1319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr20:1308000-1312000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:1308000-1313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:1308200-1317800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr20:1308400-1317000	Weak transcription	Brain Substantia Nigra	brain
25	chr20:1308800-1313200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:1308800-1315400	Weak transcription	Fetal Heart	heart
27	chr20:1308800-1316800	Weak transcription	NH-A	brain
28	chr20:1308800-1317000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:1308800-1318000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr20:1309000-1315000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:1309000-1322000	Weak transcription	HSMMtube	muscle
32	chr20:1309200-1312000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr20:1309200-1313200	Weak transcription	Osteobl	bone
34	chr20:1309600-1315400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:1309600-1317200	Weak transcription	Colon Smooth Muscle	Colon
36	chr20:1309800-1312000	Enhancers	Colonic Mucosa	Colon
37	chr20:1309800-1312000	Enhancers	Pancreas	Pancrea
38	chr20:1309800-1312400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr20:1309800-1315600	Strong transcription	Fetal Stomach	stomach
40	chr20:1309800-1335400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr20:1310000-1312000	Enhancers	Esophagus	oesophagus
42	chr20:1310000-1313000	Weak transcription	Fetal Muscle Leg	muscle
43	chr20:1310000-1313200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr20:1310000-1313400	Weak transcription	HSMM	muscle
45	chr20:1310000-1314000	Weak transcription	Hela-S3	cervix
46	chr20:1310000-1314200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr20:1310000-1316800	Weak transcription	NHLF	lung
48	chr20:1310000-1317000	Weak transcription	Brain Hippocampus Middle	brain
49	chr20:1310000-1317600	Weak transcription	Ovary	ovary
50	chr20:1310000-1348800	Weak transcription	Placenta Amnion	Placenta Amnion

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