Variant report

Variant	rs12486028
Chromosome Location	chr3:53104004-53104005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:53103860-53104010	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:53103900-53104050	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr3:53103860-53104010	HEK293	kidney:	n/a	n/a
4	CTCF	chr3:53103920-53104070	HFF-Myc	foreskin:	n/a	n/a
5	CTCF	chr3:53103860-53104010	A549	lung:	n/a	n/a
6	CTCF	chr3:53103880-53104030	HA-sp	spinal cord:	n/a	n/a
7	CTCF	chr3:53103860-53104010	HCPEpiC	choroid plexus:	n/a	n/a
8	CTCF	chr3:53103860-53104010	AoAF	blood vessel:	n/a	n/a
9	SMC3	chr3:53103747-53104014	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr3:53103920-53104070	HepG2	liver:	n/a	n/a
11	CTCF	chr3:53103860-53104010	MCF-7	breast:	n/a	n/a
12	RAD21	chr3:53103711-53104079	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:53103840-53104040	Hela-S3	cervix:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFT1-3	chr3:53100873-53109103	NONHSAT089980

No data

Variant related genes	Relation type
SERBP1P3	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12633559	1.00[AMR][1000 genomes]
rs13064076	1.00[AMR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	1.00[EUR][1000 genomes]
rs1991567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001733	1.00[EUR][1000 genomes]
rs2001734	1.00[EUR][1000 genomes]
rs2246888	1.00[EUR][1000 genomes]
rs2246889	1.00[EUR][1000 genomes]
rs2336158	1.00[EUR][1000 genomes]
rs2336159	1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336556	1.00[EUR][1000 genomes]
rs2336557	1.00[EUR][1000 genomes]
rs2336559	1.00[EUR][1000 genomes]
rs2564925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564943	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2564946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2581781	1.00[AMR][1000 genomes]
rs2581814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4234640	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	1.00[EUR][1000 genomes]
rs4687557	1.00[EUR][1000 genomes]
rs4687670	1.00[EUR][1000 genomes]
rs4687671	1.00[EUR][1000 genomes]
rs4687674	1.00[EUR][1000 genomes]
rs4687675	1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs55654539	1.00[AMR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs58561805	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs59234300	1.00[AMR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445540	1.00[EUR][1000 genomes]
rs6445542	1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs72967404	1.00[EUR][1000 genomes]
rs72967414	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629528	1.00[EUR][1000 genomes]
rs7637212	1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs9682449	1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9833487	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9869545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877711	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53098400-53106000	Weak transcription	Spleen	Spleen
2	chr3:53100400-53105800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:53100600-53106000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:53102200-53105800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53102200-53105800	Weak transcription	K562	blood
6	chr3:53102200-53106000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:53102200-53106400	Weak transcription	Colonic Mucosa	Colon
8	chr3:53102400-53106000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:53102400-53106200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:53103200-53104200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:53103600-53104200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:53103600-53104200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:53103600-53104200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:53103600-53104200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:53103600-53104200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:53103600-53104200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:53103800-53104200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:53104000-53104200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:53104000-53104200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:53104000-53106400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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