Variant report

Variant	rs6041759
Chromosome Location	chr20:1352322-1352323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1352245..1354904-chr20:1355526..1357466,3	K562	blood:
2	chr20:1351705..1353589-chr20:1357779..1360350,3	K562	blood:
3	chr20:1351555..1355162-chr20:1371278..1374408,3	MCF-7	breast:
4	chr20:1352089..1353589-chr20:1357859..1360350,2	K562	blood:
5	chr20:1303470..1306346-chr20:1351219..1354077,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234684	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1998006	1.00[MEX][hapmap]
rs41280324	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4505594	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56295224	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6033554	0.87[YRI][hapmap]
rs6033572	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6033581	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6041716	0.82[YRI][hapmap]
rs6041734	1.00[MEX][hapmap];0.87[YRI][hapmap]
rs6041772	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6041774	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6041827	1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6041846	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6041861	0.88[LWK][hapmap]
rs6041891	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6041892	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60669872	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62186862	0.90[EUR][1000 genomes]
rs62187549	0.92[EUR][1000 genomes]
rs7274574	1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs73079666	0.92[EUR][1000 genomes]
rs73079672	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1323400-1354000	Weak transcription	Fetal Heart	heart
2	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr20:1331600-1358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:1336400-1355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:1338600-1354800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
9	chr20:1345000-1353000	Weak transcription	K562	blood
10	chr20:1345600-1358000	Weak transcription	Stomach Mucosa	stomach
11	chr20:1345800-1356400	Strong transcription	Fetal Thymus	thymus
12	chr20:1346200-1356800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr20:1346600-1353000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr20:1346600-1356800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:1347000-1355600	Strong transcription	GM12878-XiMat	blood
16	chr20:1347200-1354000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr20:1347600-1354800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr20:1347600-1356400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr20:1347600-1359000	Strong transcription	Fetal Stomach	stomach
20	chr20:1347800-1355800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:1347800-1357800	Strong transcription	HepG2	liver
22	chr20:1348000-1352400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr20:1348000-1353200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
24	chr20:1348000-1353800	Strong transcription	Primary T cells from cord blood	blood
25	chr20:1348000-1354200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr20:1348000-1356200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr20:1348000-1356400	Strong transcription	Primary B cells from cord blood	blood
28	chr20:1348000-1356600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr20:1348000-1357000	Strong transcription	Thymus	Thymus
30	chr20:1348000-1366800	Strong transcription	Dnd41	blood
31	chr20:1348200-1352600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr20:1348200-1355000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr20:1348200-1355400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr20:1348200-1356000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr20:1348400-1356200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr20:1348400-1356400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr20:1349000-1362800	Weak transcription	Fetal Kidney	kidney
38	chr20:1349200-1354200	Genic enhancers	HUVEC	blood vessel
39	chr20:1349200-1354600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr20:1349400-1353000	Genic enhancers	Fetal Muscle Leg	muscle
41	chr20:1349400-1356200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr20:1349600-1356200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr20:1349800-1352600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:1349800-1353200	Weak transcription	Ovary	ovary
45	chr20:1349800-1353800	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr20:1349800-1356600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr20:1349800-1357600	Weak transcription	Small Intestine	intestine
48	chr20:1350000-1353800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:1350000-1355200	Strong transcription	Fetal Intestine Small	intestine
50	chr20:1350200-1352800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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