Variant report

Variant	rs11699339
Chromosome Location	chr20:52688306-52688307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:52688268-52688390	ProgFib	skin:	n/a	n/a
2	NR2F2	chr20:52683737-52688780	MCF-7	breast:	n/a	n/a
3	NR2F2	chr20:52682851-52688769	MCF-7	breast:	n/a	n/a
4	MAX	chr20:52682798-52688785	MCF-7	breast:	n/a	chr20:52685611-52685621

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:52688256-52688306	SK-N-SH_RA	brain:	n/a
2	chr20:52688256-52688306	HCF	heart:	n/a
3	chr20:52688256-52688306	HNPCEpiC	eye:	n/a
4	chr20:52688256-52688306	MCF10A-Er-Src	breast:	n/a
5	chr20:52688256-52688306	GM19239	blood:	n/a
6	chr20:52688256-52688306	IMR90	lung:	fetal
7	chr20:52688256-52688306	HEEpiC	esophagus:	n/a
8	chr20:52688256-52688306	HAEpiC	amniotic membrane:	n/a
9	chr20:52688256-52688306	AoSMC	blood vessel:	n/a
10	chr20:52688256-52688306	Jurkat	blood:	n/a
11	chr20:52688256-52688306	NHBE	bronchial:	n/a
12	chr20:52688256-52688306	SK-N-MC	brain:	n/a
13	chr20:52688256-52688306	ProgFib	skin:	n/a
14	chr20:52688256-52688306	SK-N-SH	brain:	n/a
15	chr20:52688256-52688306	AG04450	lung:	fetal
16	chr20:52688256-52688306	NB4	blood:	n/a
17	chr20:52688256-52688306	HRE	kidney:	n/a
18	chr20:52688256-52688306	HEK293	kidney:	embryo
19	chr20:52688256-52688306	PrEC	prostate:	n/a
20	chr20:52688256-52688306	BE2_C	brain:	n/a
21	chr20:52688256-52688306	ovcar-3	ovarian:	n/a
22	chr20:52688256-52688306	HMEC	breast:	n/a
23	chr20:52688256-52688306	SAEC	small airway:	n/a
24	chr20:52688256-52688306	PFSK-1	brain:	n/a
25	chr20:52688256-52688306	HRPEpiC	eye:	n/a
26	chr20:52688256-52688306	Hela-S3	cervix:	n/a
27	chr20:52688256-52688306	ECC-1	luminal epithelium:	n/a
28	chr20:52688256-52688306	HPAEpiC	pulmonary alveolar:	n/a
29	chr20:52688256-52688306	Caco-2	colon:	n/a
30	chr20:52688256-52688306	GM12891	blood:	n/a
31	chr20:52688256-52688306	SKMC	muscle:	n/a
32	chr20:52688256-52688306	K562	blood:	n/a
33	chr20:52688256-52688306	U87	brain:	n/a
34	chr20:52688256-52688306	PANC-1	pancreas:	n/a
35	chr20:52688256-52688306	MCF-7	breast:	n/a
36	chr20:52688256-52688306	NH-A	brain:	n/a
37	chr20:52688256-52688306	AG09319	gingival:	n/a
38	chr20:52688256-52688306	HCT-116	colon:	n/a
39	chr20:52688256-52688306	AG09309	skin:	n/a
40	chr20:52688256-52688306	HRCEpiC	kidney:	n/a
41	chr20:52688256-52688306	CMK	blood:	n/a
42	chr20:52688256-52688306	GM06990	blood:	n/a
43	chr20:52688256-52688306	NT2-D1	testis:	n/a
44	chr20:52688256-52688306	Hepatocyte	liver:	n/a
45	chr20:52688256-52688306	AG04449	skin:	fetal
46	chr20:52688256-52688306	T-47D	breast:	n/a
47	chr20:52688256-52688306	HUVEC	blood vessel:	n/a
48	chr20:52688256-52688306	HL-60	blood:	n/a
49	chr20:52688256-52688306	RPTEC	kidney:	n/a
50	chr20:52688256-52688306	A549	lung:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56734849..56737585-chr20:52685762..52689219,5	MCF-7	breast:
2	chr20:52205396..52212193-chr20:52682424..52689159,12	MCF-7	breast:
3	chr17:56734557..56739323-chr20:52682038..52691817,18	MCF-7	breast:
4	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
5	chr20:52610588..52612438-chr20:52687506..52690025,2	MCF-7	breast:
6	chr20:52682759..52688435-chr20:55837866..55842743,7	MCF-7	breast:
7	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
8	chr17:56769193..56771346-chr20:52687697..52690270,2	MCF-7	breast:
9	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
MIR4756	TF binding region
BCAS1	CpG island
MIR4756	CpG island
ENSG00000101144	Chromatin interaction
ENSG00000108384	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000121101	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13037207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531485	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1531486	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537439	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543703	0.88[YRI][hapmap]
rs290396	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs290440	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs290447	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3787547	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3787550	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs459376	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs460536	0.86[CHB][hapmap]
rs462041	0.95[CHB][hapmap]
rs462703	0.95[CHB][hapmap]
rs465096	0.90[CHB][hapmap]
rs465156	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs6064043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6064045	0.83[MEX][hapmap]
rs6068765	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6068773	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6068774	0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6068776	0.89[YRI][hapmap]
rs6512935	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv912944	chr20:52681759-52693614	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11699339	BCAS1	cis	lymphoblastoid	seeQTL
rs11699339	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52687200-52691600	Weak transcription	Gastric	stomach
2	chr20:52687400-52690000	Weak transcription	Fetal Intestine Large	intestine
3	chr20:52687400-52690400	Weak transcription	Fetal Intestine Small	intestine
4	chr20:52687400-52694000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr20:52687600-52688400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr20:52687600-52688600	Enhancers	Stomach Mucosa	stomach
7	chr20:52687600-52691200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr20:52688000-52690000	Weak transcription	HepG2	liver

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