Variant report

Variant	rs6013934
Chromosome Location	chr20:52836921-52836922
allele	C/T
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:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52835803..52837047-chr20:52936331..52937389,14	MCF-7	breast:
2	chr20:52835882..52837224-chr20:52936327..52937749,19	MCF-7	breast:
3	chr20:52835069..52840886-chr20:53069895..53074543,8	MCF-7	breast:
4	chr20:52836035..52837008-chr20:53264640..53266086,4	MCF-7	breast:
5	chr20:52834058..52838026-chr20:53082960..53086578,4	MCF-7	breast:
6	chr20:52836129..52837011-chr20:52845467..52846140,2	MCF-7	breast:
7	chr20:52815950..52816778-chr20:52836089..52837019,2	MCF-7	breast:
8	chr20:52836744..52838613-chr20:52929896..52931739,2	MCF-7	breast:
9	chr20:52834872..52837483-chr20:53257403..53260162,2	MCF-7	breast:
10	chr20:52836547..52837127-chr20:53131049..53131927,2	MCF-7	breast:
11	chr20:52834958..52838732-chr20:53262770..53264255,82	MCF-7	breast:
12	chr20:52835883..52836994-chr3:64516257..64516838,3	MCF-7	breast:
13	chr20:52836519..52837019-chr20:53065815..53066443,2	MCF-7	breast:
14	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
15	chr20:52835335..52837595-chr20:53075898..53078098,2	MCF-7	breast:
16	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
17	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
18	chr20:52836403..52837057-chr20:53261665..53262555,3	MCF-7	breast:
19	chr20:52836120..52836941-chr20:53273767..53274630,2	MCF-7	breast:
20	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:
21	chr20:52835947..52837988-chr20:53095859..53097037,10	MCF-7	breast:
22	chr1:228537810..228540414-chr20:52836573..52839154,2	MCF-7	breast:
23	chr20:52835892..52837137-chr20:53264337..53265328,4	MCF-7	breast:
24	chr20:52836354..52837037-chr20:53266035..53266658,3	MCF-7	breast:
25	chr20:52836081..52837015-chr20:53256592..53257713,5	MCF-7	breast:
26	chr20:47358616..47359172-chr20:52836118..52837006,2	MCF-7	breast:
27	chr20:52836103..52837057-chr20:53004014..53004632,4	MCF-7	breast:
28	chr20:52836304..52836988-chr20:52968140..52968678,2	MCF-7	breast:
29	chr20:52713391..52714001-chr20:52836194..52836975,2	MCF-7	breast:
30	chr20:52836430..52839312-chr20:53251846..53253963,2	MCF-7	breast:
31	chr20:52835324..52837419-chr20:53262103..53264598,40	MCF-7	breast:
32	chr20:52836080..52837145-chr20:52888954..52890297,11	MCF-7	breast:
33	chr20:52823575..52825303-chr20:52835927..52837987,2	K562	blood:
34	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]
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]
rs6023047	1.00[AFR][1000 genomes];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:117 , 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	chr20:52826000-52837200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:52826000-52837800	Weak transcription	Fetal Thymus	thymus
5	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
6	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52826200-52838800	Weak transcription	Gastric	stomach
8	chr20:52826600-52837400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr20:52826600-52838200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr20:52826600-52838800	Weak transcription	Brain Anterior Caudate	brain
11	chr20:52826800-52837200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:52826800-52838200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr20:52826800-52838400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:52826800-52838800	Weak transcription	Brain Hippocampus Middle	brain
15	chr20:52827000-52838400	Weak transcription	Fetal Brain Male	brain
16	chr20:52827000-52838800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr20:52827000-52838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr20:52827000-52838800	Weak transcription	Fetal Lung	lung
19	chr20:52827000-52838800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr20:52827200-52838800	Weak transcription	Right Atrium	heart
21	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
22	chr20:52829200-52837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
24	chr20:52829600-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr20:52829600-52838800	Weak transcription	NH-A	brain
26	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr20:52829800-52837800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr20:52830000-52838800	Weak transcription	NHDF-Ad	bronchial
29	chr20:52830000-52839200	Weak transcription	Ovary	ovary
30	chr20:52830600-52837000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr20:52830800-52837400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr20:52832200-52838600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr20:52832600-52837800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr20:52832600-52838000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr20:52832800-52838600	Weak transcription	HMEC	breast
37	chr20:52833000-52838200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr20:52833000-52838200	Weak transcription	Fetal Kidney	kidney
39	chr20:52833000-52838600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:52834000-52838200	Weak transcription	Esophagus	oesophagus
42	chr20:52834000-52838800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr20:52834000-52838800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:52834200-52837000	Weak transcription	A549	lung
45	chr20:52834200-52837200	Weak transcription	Fetal Brain Female	brain
46	chr20:52834200-52837600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr20:52834200-52837800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr20:52834200-52838800	Weak transcription	Fetal Intestine Large	intestine
49	chr20:52834200-52839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr20:52834200-52839000	Weak transcription	Brain Angular Gyrus	brain

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