Variant report

Variant	rs6023047
Chromosome Location	chr20:52837909-52837910
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52835069..52840886-chr20:53069895..53074543,8	MCF-7	breast:
2	chr20:52834058..52838026-chr20:53082960..53086578,4	MCF-7	breast:
3	chr20:52836744..52838613-chr20:52929896..52931739,2	MCF-7	breast:
4	chr20:52834958..52838732-chr20:53262770..53264255,82	MCF-7	breast:
5	chr20:52837538..52838039-chr7:155137508..155138181,2	MCF-7	breast:
6	chr20:52837790..52839838-chr20:53004656..53006730,2	MCF-7	breast:
7	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
8	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
9	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
10	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:
11	chr20:52837894..52838793-chr20:52889468..52890085,3	MCF-7	breast:
12	chr20:52835947..52837988-chr20:53095859..53097037,10	MCF-7	breast:
13	chr1:228537810..228540414-chr20:52836573..52839154,2	MCF-7	breast:
14	chr20:52837337..52840650-chr20:52960350..52963395,3	MCF-7	breast:
15	chr20:52836430..52839312-chr20:53251846..53253963,2	MCF-7	breast:
16	chr20:52823575..52825303-chr20:52835927..52837987,2	K562	blood:
17	chr20:52837175..52839951-chr20:52903324..52905854,2	MCF-7	breast:
18	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs367149	1.00[EUR][1000 genomes]
rs372987	1.00[EUR][1000 genomes]
rs374623	1.00[EUR][1000 genomes]
rs377448	1.00[EUR][1000 genomes]
rs378666	1.00[EUR][1000 genomes]
rs378668	1.00[EUR][1000 genomes]
rs380980	1.00[EUR][1000 genomes]
rs383890	1.00[EUR][1000 genomes]
rs389806	1.00[EUR][1000 genomes]
rs393866	1.00[EUR][1000 genomes]
rs396957	1.00[EUR][1000 genomes]
rs404705	1.00[EUR][1000 genomes]
rs406389	1.00[EUR][1000 genomes]
rs414058	1.00[EUR][1000 genomes]
rs415230	1.00[EUR][1000 genomes]
rs416263	1.00[EUR][1000 genomes]
rs416724	1.00[EUR][1000 genomes]
rs418191	1.00[EUR][1000 genomes]
rs422615	1.00[EUR][1000 genomes]
rs422818	1.00[EUR][1000 genomes]
rs423338	1.00[EUR][1000 genomes]
rs424195	1.00[EUR][1000 genomes]
rs425792	1.00[EUR][1000 genomes]
rs429350	1.00[EUR][1000 genomes]
rs437970	1.00[EUR][1000 genomes]
rs446835	1.00[EUR][1000 genomes]
rs6013929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6013931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6013932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6013934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6127144	1.00[EUR][1000 genomes]
rs73285988	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52825400-52838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:52825600-52839000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
4	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:52826200-52838800	Weak transcription	Gastric	stomach
6	chr20:52826600-52838200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:52826600-52838800	Weak transcription	Brain Anterior Caudate	brain
8	chr20:52826800-52838200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:52826800-52838400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:52826800-52838800	Weak transcription	Brain Hippocampus Middle	brain
11	chr20:52827000-52838400	Weak transcription	Fetal Brain Male	brain
12	chr20:52827000-52838800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr20:52827000-52838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr20:52827000-52838800	Weak transcription	Fetal Lung	lung
15	chr20:52827000-52838800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:52827200-52838800	Weak transcription	Right Atrium	heart
17	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
18	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
19	chr20:52829600-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr20:52829600-52838800	Weak transcription	NH-A	brain
21	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr20:52830000-52838800	Weak transcription	NHDF-Ad	bronchial
23	chr20:52830000-52839200	Weak transcription	Ovary	ovary
24	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr20:52832200-52838600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr20:52832600-52838000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr20:52832800-52838600	Weak transcription	HMEC	breast
28	chr20:52833000-52838200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:52833000-52838200	Weak transcription	Fetal Kidney	kidney
30	chr20:52833000-52838600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr20:52834000-52838200	Weak transcription	Esophagus	oesophagus
33	chr20:52834000-52838800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr20:52834000-52838800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr20:52834200-52838800	Weak transcription	Fetal Intestine Large	intestine
36	chr20:52834200-52839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:52834200-52839000	Weak transcription	Brain Angular Gyrus	brain
38	chr20:52834200-52840800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr20:52834200-52841000	Weak transcription	Primary B cells from cord blood	blood
40	chr20:52834200-52841200	Weak transcription	Spleen	Spleen
41	chr20:52834200-52843600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr20:52834400-52838200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr20:52834400-52838800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr20:52834400-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:52834600-52838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr20:52834600-52838200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr20:52834600-52838200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr20:52834600-52838800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr20:52834600-52838800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr20:52834600-52840000	Weak transcription	Psoas Muscle	Psoas

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