Variant report

Variant	rs28739569
Chromosome Location	chr1:223898499-223898500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:223898086-223898664	HepG2	liver:	n/a	n/a
2	JUND	chr1:223898200-223898532	K562	blood:	n/a	n/a
3	HDAC2	chr1:223898230-223898630	HepG2	liver:	n/a	n/a
4	TEAD4	chr1:223898094-223898585	K562	blood:	n/a	n/a
5	CEBPD	chr1:223898086-223898512	K562	blood:	n/a	n/a
6	MYC	chr1:223898153-223898707	K562	blood:	n/a	n/a
7	FOXA1	chr1:223898164-223898681	HepG2	liver:	n/a	n/a
8	TEAD4	chr1:223898087-223898582	K562	blood:	n/a	n/a
9	FOXA2	chr1:223898173-223898601	HepG2	liver:	n/a	n/a
10	GATA2	chr1:223898092-223898557	K562	blood:	n/a	n/a
11	NFIC	chr1:223898170-223898499	HepG2	liver:	n/a	n/a
12	CUX1	chr1:223898228-223898532	K562	blood:	n/a	n/a
13	FOXA1	chr1:223898205-223898667	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:223898211-223898521	K562	blood:	n/a	n/a
15	EP300	chr1:223898180-223898515	K562	blood:	n/a	n/a
16	HDAC2	chr1:223898210-223898621	HepG2	liver:	n/a	n/a
17	EP300	chr1:223898160-223898600	HepG2	liver:	n/a	n/a
18	TCF7L2	chr1:223898131-223898605	HEK293	kidney:	n/a	n/a
19	FOXA1	chr1:223898241-223898637	HepG2	liver:	n/a	n/a
20	FOXA1	chr1:223898212-223898600	HepG2	liver:	n/a	n/a
21	RCOR1	chr1:223898150-223898561	K562	blood:	n/a	n/a
22	TAL1	chr1:223898176-223898585	K562	blood:	n/a	n/a
23	TCF7L2	chr1:223898237-223898509	HepG2	liver:	n/a	n/a
24	ZMIZ1	chr1:223898198-223898514	K562	blood:	n/a	n/a
25	JUN	chr1:223898325-223898525	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223886668..223890344-chr1:223897746..223900327,3	K562	blood:
2	chr1:223882393..223884567-chr1:223898139..223900023,2	MCF-7	breast:
3	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
4	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
5	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10799550	0.83[EUR][1000 genomes]
rs10916600	0.95[EUR][1000 genomes]
rs10916601	0.96[EUR][1000 genomes]
rs10916602	0.96[EUR][1000 genomes]
rs10916603	0.95[EUR][1000 genomes]
rs10916634	0.92[EUR][1000 genomes]
rs10916646	0.92[EUR][1000 genomes]
rs11580460	0.92[EUR][1000 genomes]
rs12070364	0.92[EUR][1000 genomes]
rs12074091	0.96[EUR][1000 genomes]
rs12567519	0.81[EUR][1000 genomes]
rs12568612	0.81[EUR][1000 genomes]
rs1419305	0.92[EUR][1000 genomes]
rs1539707	0.88[EUR][1000 genomes]
rs17556570	0.81[EUR][1000 genomes]
rs1779658	0.87[EUR][1000 genomes]
rs1892076	0.95[EUR][1000 genomes]
rs1892077	0.96[EUR][1000 genomes]
rs2186006	0.96[EUR][1000 genomes]
rs28370014	0.95[EUR][1000 genomes]
rs4511081	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653499	0.96[EUR][1000 genomes]
rs4653500	0.95[EUR][1000 genomes]
rs61822636	0.81[EUR][1000 genomes]
rs61823962	0.84[EUR][1000 genomes]
rs61823965	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61823966	0.96[EUR][1000 genomes]
rs61823967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823980	0.92[EUR][1000 genomes]
rs61823981	0.92[EUR][1000 genomes]
rs6669046	0.92[EUR][1000 genomes]
rs6674733	0.92[EUR][1000 genomes]
rs6702314	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702430	0.85[EUR][1000 genomes]
rs7412088	0.95[EUR][1000 genomes]
rs7414311	0.96[EUR][1000 genomes]
rs7517684	0.90[EUR][1000 genomes]
rs7525446	0.92[EUR][1000 genomes]
rs7547642	0.90[EUR][1000 genomes]
rs7555491	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28739569	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223891200-223898600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:223893000-223898800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:223893400-223899600	Weak transcription	Fetal Kidney	kidney
6	chr1:223894000-223898600	Weak transcription	Fetal Brain Female	brain
7	chr1:223894000-223899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:223894000-223899800	Enhancers	Fetal Intestine Large	intestine
9	chr1:223894600-223898600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:223894600-223899000	Weak transcription	Fetal Brain Male	brain
11	chr1:223895400-223899400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:223895600-223898800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:223895600-223898800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:223895600-223899000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:223895600-223899000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:223895600-223899400	Weak transcription	Esophagus	oesophagus
17	chr1:223895600-223899600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:223895600-223899600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:223895600-223899800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:223895800-223899000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:223895800-223899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:223895800-223899600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:223895800-223899600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:223895800-223899600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:223895800-223899600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:223895800-223899600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:223895800-223899600	Weak transcription	Right Ventricle	heart
28	chr1:223895800-223899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:223896000-223898800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:223896000-223898800	Weak transcription	Fetal Stomach	stomach
31	chr1:223896000-223898800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:223896000-223899000	Enhancers	A549	lung
33	chr1:223896000-223899400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:223896000-223899400	Weak transcription	Pancreas	Pancrea
35	chr1:223896000-223899600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:223896000-223899600	Weak transcription	Aorta	Aorta
37	chr1:223896000-223899600	Weak transcription	Colonic Mucosa	Colon
38	chr1:223896000-223899600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:223896000-223899600	Weak transcription	Ovary	ovary
40	chr1:223896000-223899800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:223896000-223899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:223896000-223899800	Weak transcription	Left Ventricle	heart
43	chr1:223896000-223899800	Weak transcription	Psoas Muscle	Psoas
44	chr1:223896000-223900000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:223896000-223900200	Weak transcription	Small Intestine	intestine
46	chr1:223896200-223898800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:223896200-223899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:223896400-223898800	Weak transcription	Gastric	stomach
49	chr1:223896800-223898600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:223896800-223898800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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