Variant report

Variant	rs6068691
Chromosome Location	chr20:52469400-52469401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:115213264..115215314-chr20:52468721..52470808,2	MCF-7	breast:
2	chr20:52466894..52469692-chr20:52471207..52473335,2	K562	blood:
3	chr20:52468474..52471005-chr3:17134540..17137301,2	MCF-7	breast:
4	chr17:57969168..57971185-chr20:52467018..52469521,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFDN4-6	chr20:52469245-52470170	NONHSAT080408

Variant related genes	Relation type
ENSG00000108423	Chromatin interaction
ENSG00000108443	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10432728	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809941	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4809942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4811476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6013809	0.81[JPT][hapmap]
rs6022786	0.81[JPT][hapmap]
rs6064011	1.00[JPT][hapmap]
rs6068688	0.93[EUR][1000 genomes]
rs6068690	0.98[ASN][1000 genomes]
rs6097618	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs6097632	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6126982	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs6126985	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6126986	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs720387	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	esv18025	chr20:52464720-52486135	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
2	chr20:52456600-52476200	Weak transcription	Gastric	stomach
3	chr20:52459600-52472600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52463000-52474000	Weak transcription	A549	lung
5	chr20:52464400-52472400	Weak transcription	Fetal Stomach	stomach
6	chr20:52464600-52472800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:52464600-52474200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:52465200-52472000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:52465200-52472000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:52465200-52472200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr20:52465200-52472200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:52465200-52472400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr20:52466200-52472200	Weak transcription	Thymus	Thymus
14	chr20:52467200-52471600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr20:52467200-52472600	Weak transcription	Adipose Nuclei	Adipose
16	chr20:52467400-52469400	Weak transcription	GM12878-XiMat	blood
17	chr20:52467400-52471600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr20:52467400-52471600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr20:52467600-52472200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr20:52468400-52470000	Enhancers	HepG2	liver
21	chr20:52468600-52471600	Weak transcription	Primary T cells from cord blood	blood
22	chr20:52468800-52471600	Weak transcription	Fetal Thymus	thymus
23	chr20:52468800-52471800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:52468800-52471800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr20:52468800-52472200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr20:52468800-52472200	Weak transcription	Dnd41	blood
27	chr20:52468800-52474400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr20:52468800-52474400	Weak transcription	Colonic Mucosa	Colon
29	chr20:52468800-52476200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr20:52468800-52481400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:52469000-52474200	Weak transcription	K562	blood
32	chr20:52469000-52474200	Weak transcription	NHEK	skin
33	chr20:52469400-52470000	Enhancers	GM12878-XiMat	blood

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