Variant report

Variant	rs2286306
Chromosome Location	chr20:52558849-52558850
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:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
2	chr20:52557853..52560053-chr20:52573644..52576413,2	K562	blood:
3	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
4	chr20:46413293..46415823-chr20:52557677..52560611,2	MCF-7	breast:
5	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
6	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
7	chr17:56707751..56710392-chr20:52555190..52558925,4	MCF-7	breast:
8	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
9	chr20:52494576..52495179-chr20:52558539..52559209,2	MCF-7	breast:
10	chr17:59489843..59492538-chr20:52557995..52559827,2	MCF-7	breast:
11	chr17:59821647..59823394-chr20:52558148..52560455,2	MCF-7	breast:
12	chr17:56756569..56758414-chr20:52557651..52559587,2	MCF-7	breast:
13	chr20:52558114..52560267-chr20:55792909..55794568,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFDN4-1	chr20:52558714-52559047	XLOC_013571

No data

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2276516	1.00[YRI][hapmap]
rs3185586	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6068729	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6123328	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes]
rs6123330	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6127021	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs886856	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286306	BCAS1	cis	brain	BrainEAC

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:52552800-52560200	Weak transcription	Primary T cells from cord blood	blood
6	chr20:52552800-52560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr20:52554200-52559200	Enhancers	K562	blood
8	chr20:52554600-52560000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
11	chr20:52555200-52559400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr20:52555400-52559400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:52555400-52561000	Enhancers	Fetal Heart	heart
14	chr20:52555800-52559000	Enhancers	Colon Smooth Muscle	Colon
15	chr20:52556000-52559200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr20:52556000-52559200	Enhancers	Fetal Muscle Leg	muscle
17	chr20:52556000-52560400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr20:52556400-52559000	Enhancers	NHDF-Ad	bronchial
19	chr20:52556400-52560800	Enhancers	Primary B cells from cord blood	blood
20	chr20:52556400-52561000	Enhancers	Fetal Lung	lung
21	chr20:52556400-52564000	Weak transcription	Esophagus	oesophagus
22	chr20:52556400-52564000	Weak transcription	Gastric	stomach
23	chr20:52556400-52565400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr20:52556600-52559400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:52556600-52559600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:52556600-52566000	Weak transcription	Aorta	Aorta
27	chr20:52556800-52559400	Flanking Active TSS	GM12878-XiMat	blood
28	chr20:52556800-52564000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr20:52557000-52559800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr20:52557000-52560000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr20:52557000-52560200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr20:52557000-52560400	Enhancers	Fetal Stomach	stomach
33	chr20:52557000-52560600	Weak transcription	NHEK	skin
34	chr20:52557000-52564200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr20:52557200-52559000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:52557200-52559200	Enhancers	Fetal Thymus	thymus
37	chr20:52557200-52559800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr20:52557200-52560000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:52557200-52560600	Weak transcription	Hela-S3	cervix
40	chr20:52557200-52565000	Weak transcription	Left Ventricle	heart
41	chr20:52557400-52559200	Weak transcription	Liver	Liver
42	chr20:52557400-52559400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr20:52557400-52560400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr20:52557800-52559000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr20:52557800-52559000	Enhancers	Fetal Muscle Trunk	muscle
47	chr20:52557800-52559000	Enhancers	HSMMtube	muscle
48	chr20:52557800-52559200	Enhancers	NH-A	brain
49	chr20:52557800-52559400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr20:52557800-52559800	Weak transcription	HMEC	breast

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