Variant report

Variant	rs51301
Chromosome Location	chr20:52838271-52838272
allele	G/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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52835069..52840886-chr20:53069895..53074543,8	MCF-7	breast:
2	chr20:52836744..52838613-chr20:52929896..52931739,2	MCF-7	breast:
3	chr20:52838097..52840122-chr20:52937035..52938814,2	MCF-7	breast:
4	chr20:52834958..52838732-chr20:53262770..53264255,82	MCF-7	breast:
5	chr20:52837790..52839838-chr20:53004656..53006730,2	MCF-7	breast:
6	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
7	chr20:52830354..52840699-chr20:53260794..53267992,26	MCF-7	breast:
8	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
9	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:
10	chr20:52837894..52838793-chr20:52889468..52890085,3	MCF-7	breast:
11	chr20:45988897..45990443-chr20:52838117..52840797,2	MCF-7	breast:
12	chr1:228537810..228540414-chr20:52836573..52839154,2	MCF-7	breast:
13	chr20:52837337..52840650-chr20:52960350..52963395,3	MCF-7	breast:
14	chr20:52836430..52839312-chr20:53251846..53253963,2	MCF-7	breast:
15	chr20:52837175..52839951-chr20:52903324..52905854,2	MCF-7	breast:
16	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:

No data

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1293132	0.81[CEU][hapmap]
rs1418925	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2585417	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2585418	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs292113	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs292118	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs3479	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs368933	0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs391235	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs422257	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs441506	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6013925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6013944	0.81[CEU][hapmap]
rs6091837	0.85[ASN][1000 genomes]
rs6127138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][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:114 , 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	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:52826200-52838800	Weak transcription	Gastric	stomach
5	chr20:52826600-52838800	Weak transcription	Brain Anterior Caudate	brain
6	chr20:52826800-52838400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52826800-52838800	Weak transcription	Brain Hippocampus Middle	brain
8	chr20:52827000-52838400	Weak transcription	Fetal Brain Male	brain
9	chr20:52827000-52838800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr20:52827000-52838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:52827000-52838800	Weak transcription	Fetal Lung	lung
12	chr20:52827000-52838800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr20:52827200-52838800	Weak transcription	Right Atrium	heart
14	chr20:52827200-52841000	Weak transcription	Brain Germinal Matrix	brain
15	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
16	chr20:52829600-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:52829600-52838800	Weak transcription	NH-A	brain
18	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:52830000-52838800	Weak transcription	NHDF-Ad	bronchial
20	chr20:52830000-52839200	Weak transcription	Ovary	ovary
21	chr20:52831400-52842200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr20:52832200-52838600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr20:52832800-52838600	Weak transcription	HMEC	breast
24	chr20:52833000-52838600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:52834000-52838800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr20:52834000-52838800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:52834200-52838800	Weak transcription	Fetal Intestine Large	intestine
29	chr20:52834200-52839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:52834200-52839000	Weak transcription	Brain Angular Gyrus	brain
31	chr20:52834200-52840800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr20:52834200-52841000	Weak transcription	Primary B cells from cord blood	blood
33	chr20:52834200-52841200	Weak transcription	Spleen	Spleen
34	chr20:52834200-52843600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr20:52834400-52838800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr20:52834400-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:52834600-52838800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr20:52834600-52838800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr20:52834600-52840000	Weak transcription	Psoas Muscle	Psoas
40	chr20:52834600-52840600	Weak transcription	Lung	lung
41	chr20:52834600-52840600	Weak transcription	Thymus	Thymus
42	chr20:52834600-52843600	Weak transcription	GM12878-XiMat	blood
43	chr20:52834600-52845200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr20:52834600-52845200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr20:52834600-52845200	Weak transcription	NHEK	skin
46	chr20:52834800-52839000	Weak transcription	NHLF	lung
47	chr20:52835200-52838400	Weak transcription	Primary T cells from cord blood	blood
48	chr20:52835200-52838800	Weak transcription	Left Ventricle	heart
49	chr20:52835200-52838800	Weak transcription	Right Ventricle	heart
50	chr20:52835600-52838400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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