Variant report

Variant	rs28365115
Chromosome Location	chr3:53778620-53778621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:53778411-53778736	H1-hESC	embryonic stem cell:	n/a	n/a
2	SMC3	chr3:53778469-53778648	GM12878	blood:	n/a	n/a
3	CTCF	chr3:53778484-53778668	GM12891	blood:	n/a	n/a
4	CTCF	chr3:53778480-53778630	HMEC	breast:	n/a	n/a
5	CTCF	chr3:53778505-53778665	MCF-7	breast:	n/a	n/a
6	CTCF	chr3:53778500-53778650	GM12874	blood:	n/a	n/a
7	CTCF	chr3:53778438-53778706	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr3:53778464-53778695	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF3	chr3:53778452-53778737	GM12878	blood:	n/a	n/a
10	CTCF	chr3:53778525-53778667	MCF-7	breast:	n/a	n/a
11	MAX	chr3:53778406-53778729	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:53778480-53778630	GM12873	blood:	n/a	n/a
13	MAX	chr3:53778358-53778877	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:53778540-53778690	HEK293	kidney:	n/a	n/a
15	CTCF	chr3:53778480-53778630	A549	lung:	n/a	n/a
16	CTCF	chr3:53778480-53778630	HCPEpiC	choroid plexus:	n/a	n/a
17	TCF12	chr3:53778452-53778682	GM12878	blood:	n/a	n/a
18	CTCF	chr3:53778539-53778669	GM12892	blood:	n/a	n/a
19	CTCF	chr3:53778493-53778683	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:53778471-53778697	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:53778480-53778630	GM12871	blood:	n/a	n/a
22	POLR2A	chr3:53778569-53778650	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr3:53778458-53778818	GM12878	blood:	n/a	n/a
24	CTCF	chr3:53778480-53778630	GM12878	blood:	n/a	n/a
25	CTCF	chr3:53778480-53778630	Caco-2	colon:	n/a	n/a
26	MYC	chr3:53778551-53778673	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:53778560-53778710	GM12869	blood:	n/a	n/a
28	CTCF	chr3:53778599-53778623	GM12878	blood:	n/a	n/a
29	MAX	chr3:53778471-53778825	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr3:53778540-53778690	GM12868	blood:	n/a	n/a
31	CTCF	chr3:53778520-53778670	GM12873	blood:	n/a	n/a
32	CTCF	chr3:53778520-53778670	GM12872	blood:	n/a	n/a
33	BATF	chr3:53778467-53778708	GM12878	blood:	n/a	n/a
34	CTCF	chr3:53778500-53778650	Caco-2	colon:	n/a	n/a
35	CTCF	chr3:53778480-53778630	GM12866	blood:	n/a	n/a
36	CTCF	chr3:53778520-53778670	HCT-116	colon:	n/a	n/a
37	CTCF	chr3:53778500-53778650	GM12875	blood:	n/a	n/a
38	CTCF	chr3:53778480-53778630	GM12868	blood:	n/a	n/a
39	CTCF	chr3:53778480-53778630	GM12867	blood:	n/a	n/a
40	CTCF	chr3:53778500-53778650	GM12873	blood:	n/a	n/a
41	CTCF	chr3:53778500-53778650	GM12865	blood:	n/a	n/a
42	CTCF	chr3:53778480-53778630	WERI-Rb-1	eye:	n/a	n/a
43	CTCF	chr3:53778520-53778670	GM06990	blood:	n/a	n/a
44	CTCF	chr3:53778560-53778710	GM12874	blood:	n/a	n/a
45	RAD21	chr3:53778379-53778780	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr3:53778519-53778663	GM19239	blood:	n/a	n/a
47	MAX	chr3:53778455-53778736	ECC-1	luminal epithelium:	n/a	n/a
48	CTCF	chr3:53778395-53778762	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr3:53778480-53778630	GM06990	blood:	n/a	n/a
50	CTCF	chr3:53778540-53778690	SK-N-SH_RA	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53777857..53780018-chr3:53784994..53786883,2	K562	blood:

No data

Variant related genes	Relation type
CACNA1D	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11719163	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11918583	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434705	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3733070	0.81[EUR][1000 genomes]
rs3774558	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3774567	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774570	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3774577	0.83[EUR][1000 genomes]
rs3774580	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3821860	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3821866	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846215	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41276449	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56384446	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776947	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797014	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs714786	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9311514	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
2	chr3:53764200-53779800	Weak transcription	Liver	Liver
3	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
7	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:53766600-53781200	Weak transcription	Lung	lung
10	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
11	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
15	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53775800-53779400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:53777800-53778800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:53777800-53779000	Enhancers	Fetal Thymus	thymus
21	chr3:53777800-53787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:53778000-53778800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:53778000-53778800	Enhancers	Pancreas	Pancrea
24	chr3:53778000-53778800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:53778000-53779800	Enhancers	GM12878-XiMat	blood
26	chr3:53778400-53778800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:53778400-53778800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:53778400-53778800	Enhancers	Psoas Muscle	Psoas
29	chr3:53778400-53779000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:53778400-53779000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr3:53778400-53781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:53778400-53781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:53778600-53778800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum

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