Variant report

Variant	rs6013930
Chromosome Location	chr20:52831496-52831497
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52829101..52831108-chr20:52831173..52832782,2	K562	blood:
2	chr20:52830268..52836346-chr20:52932384..52936332,6	MCF-7	breast:
3	chr20:52830853..52833547-chr20:52972532..52974681,2	MCF-7	breast:
4	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
5	chr17:79479285..79481012-chr20:52830977..52833560,2	MCF-7	breast:
6	chr20:52829436..52832401-chr20:53250879..53253228,2	MCF-7	breast:
7	chr20:52828484..52831643-chr20:53256880..53260279,4	MCF-7	breast:
8	chr20:52830936..52833739-chr20:52871496..52873804,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229947	Chromatin interaction
ENSG00000184009	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16999466	1.00[CEU][hapmap]
rs2219733	1.00[CEU][hapmap]
rs6013926	0.83[TSI][hapmap]
rs6013977	1.00[CEU][hapmap]
rs6023037	1.00[EUR][1000 genomes]
rs6023065	0.85[EUR][1000 genomes]
rs6023109	1.00[CEU][hapmap]
rs6023118	1.00[CEU][hapmap]
rs6023119	1.00[CEU][hapmap]
rs6023120	1.00[CEU][hapmap]
rs6023128	1.00[CEU][hapmap]
rs6023139	1.00[CEU][hapmap]
rs6097840	1.00[TSI][hapmap]
rs73135202	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73137415	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7347628	1.00[CEU][hapmap]

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:123 , 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	chr20:52825600-52833800	Weak transcription	Lung	lung
3	chr20:52825600-52839000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:52826000-52833400	Weak transcription	Esophagus	oesophagus
5	chr20:52826000-52833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:52826000-52837200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:52826000-52837800	Weak transcription	Fetal Thymus	thymus
8	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
9	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:52826200-52831800	Weak transcription	Fetal Kidney	kidney
11	chr20:52826200-52836000	Weak transcription	Colonic Mucosa	Colon
12	chr20:52826200-52838800	Weak transcription	Gastric	stomach
13	chr20:52826400-52831600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr20:52826400-52831600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:52826400-52831800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:52826600-52831600	Weak transcription	Placenta	Placenta
17	chr20:52826600-52831600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr20:52826600-52832200	Weak transcription	Left Ventricle	heart
19	chr20:52826600-52832400	Weak transcription	GM12878-XiMat	blood
20	chr20:52826600-52833600	Weak transcription	Spleen	Spleen
21	chr20:52826600-52836800	Weak transcription	Liver	Liver
22	chr20:52826600-52837400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr20:52826600-52838200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr20:52826600-52838800	Weak transcription	Brain Anterior Caudate	brain
25	chr20:52826800-52832000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr20:52826800-52833600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:52826800-52833600	Weak transcription	Brain Angular Gyrus	brain
28	chr20:52826800-52837200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr20:52826800-52838200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr20:52826800-52838400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:52826800-52838800	Weak transcription	Brain Hippocampus Middle	brain
32	chr20:52827000-52831800	Weak transcription	Adipose Nuclei	Adipose
33	chr20:52827000-52833200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr20:52827000-52833200	Weak transcription	Fetal Intestine Small	intestine
35	chr20:52827000-52836200	Weak transcription	Small Intestine	intestine
36	chr20:52827000-52838400	Weak transcription	Fetal Brain Male	brain
37	chr20:52827000-52838800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr20:52827000-52838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr20:52827000-52838800	Weak transcription	Fetal Lung	lung
40	chr20:52827000-52838800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr20:52827200-52838800	Weak transcription	Right Atrium	heart
42	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
43	chr20:52828400-52831800	Weak transcription	Fetal Brain Female	brain
44	chr20:52828400-52832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr20:52829200-52833800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:52829200-52834000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr20:52829200-52837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr20:52829400-52831800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr20:52829400-52833800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr20:52829400-52835800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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