Variant report

Variant	rs2896828
Chromosome Location	chr1:223898685-223898686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr1:223898669-223899076	K562	blood:	n/a	n/a
2	MYC	chr1:223898153-223898707	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223886668..223890344-chr1:223897746..223900327,3	K562	blood:
2	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
3	chr1:223882393..223884567-chr1:223898139..223900023,2	MCF-7	breast:
4	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
5	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
6	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
7	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: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10916600	0.84[ASN][1000 genomes]
rs10916603	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1892076	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2040103	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186006	0.83[AFR][1000 genomes]
rs28370014	0.82[AFR][1000 genomes]
rs4233224	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653834	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683379	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7412088	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7414311	0.83[AFR][1000 genomes]
rs7524132	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539624	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554857	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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
rs2896828	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 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	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:223893000-223898800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:223893400-223899600	Weak transcription	Fetal Kidney	kidney
5	chr1:223894000-223899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:223894000-223899800	Enhancers	Fetal Intestine Large	intestine
7	chr1:223894600-223899000	Weak transcription	Fetal Brain Male	brain
8	chr1:223895400-223899400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:223895600-223898800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:223895600-223898800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:223895600-223899000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:223895600-223899000	Weak transcription	Brain Substantia Nigra	brain
13	chr1:223895600-223899400	Weak transcription	Esophagus	oesophagus
14	chr1:223895600-223899600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:223895600-223899600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:223895600-223899800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:223895800-223899000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:223895800-223899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:223895800-223899600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:223895800-223899600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:223895800-223899600	Weak transcription	Brain Anterior Caudate	brain
22	chr1:223895800-223899600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:223895800-223899600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:223895800-223899600	Weak transcription	Right Ventricle	heart
25	chr1:223895800-223899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:223896000-223898800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:223896000-223898800	Weak transcription	Fetal Stomach	stomach
28	chr1:223896000-223898800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:223896000-223899000	Enhancers	A549	lung
30	chr1:223896000-223899400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:223896000-223899400	Weak transcription	Pancreas	Pancrea
32	chr1:223896000-223899600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:223896000-223899600	Weak transcription	Aorta	Aorta
34	chr1:223896000-223899600	Weak transcription	Colonic Mucosa	Colon
35	chr1:223896000-223899600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:223896000-223899600	Weak transcription	Ovary	ovary
37	chr1:223896000-223899800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:223896000-223899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:223896000-223899800	Weak transcription	Left Ventricle	heart
40	chr1:223896000-223899800	Weak transcription	Psoas Muscle	Psoas
41	chr1:223896000-223900000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:223896000-223900200	Weak transcription	Small Intestine	intestine
43	chr1:223896200-223898800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:223896200-223899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:223896400-223898800	Weak transcription	Gastric	stomach
46	chr1:223896800-223898800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:223896800-223898800	Weak transcription	NH-A	brain
48	chr1:223896800-223899000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:223896800-223899800	Weak transcription	Placenta	Placenta
50	chr1:223897000-223898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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