Variant report

Variant	rs4653836
Chromosome Location	chr1:223887895-223887896
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr1:223887609-223889555	IMR90	lung:	n/a	n/a
2	SP1	chr1:223887877-223889525	A549	lung:	n/a	chr1:223889183-223889190 chr1:223888840-223888849
3	POLR2A	chr1:223887855-223891488	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:223887883-223896154	U87	brain:	n/a	n/a
5	MAZ	chr1:223887862-223889552	IMR90	lung:	n/a	chr1:223888049-223888059
6	TCF12	chr1:223887740-223889537	A549	lung:	n/a	chr1:223888946-223888953
7	JUN	chr1:223887458-223889515	K562	blood:	n/a	chr1:223888799-223888807 chr1:223889155-223889163 chr1:223888795-223888806 chr1:223888797-223888809
8	MAX	chr1:223887881-223889524	A549	lung:	n/a	chr1:223888049-223888059
9	NR3C1	chr1:223887828-223889375	A549	lung:	n/a	chr1:223888427-223888441 chr1:223889119-223889128 chr1:223887845-223887871 chr1:223888426-223888442 chr1:223888426-223888442 chr1:223887845-223887871 chr1:223888426-223888442 chr1:223888426-223888442 chr1:223888427-223888441 chr1:223887845-223887871 chr1:223887845-223887871 chr1:223888161-223888168

No.	Distal block	Cell Line	Cell type
1	chr1:223886668..223890344-chr1:223897746..223900327,3	K562	blood:
2	chr1:223886105..223888614-chr1:223940802..223943504,3	K562	blood:
3	chr1:223886106..223888847-chr1:223934489..223936535,2	K562	blood:
4	chr1:223886322..223888614-chr1:223940802..223943504,2	K562	blood:
5	chr1:223884342..223885890-chr1:223887258..223888847,2	K562	blood:
6	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
7	chr1:223886106..223889532-chr1:223933715..223936535,3	K562	blood:

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

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2000319	0.82[AFR][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
rs4653836	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223884000-223888400	Weak transcription	Right Atrium	heart
2	chr1:223884200-223888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:223884400-223888400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:223884400-223888800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:223884400-223888800	Weak transcription	Pancreas	Pancrea
6	chr1:223885600-223888400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:223885800-223888600	Enhancers	NHDF-Ad	bronchial
8	chr1:223886000-223888400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:223886200-223888000	Enhancers	Hela-S3	cervix
10	chr1:223886200-223888400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:223886200-223888400	Enhancers	HMEC	breast
12	chr1:223886200-223888600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:223886200-223889400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:223886200-223889400	Enhancers	Placenta	Placenta
15	chr1:223886400-223888000	Weak transcription	Adipose Nuclei	Adipose
16	chr1:223886400-223888200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:223886400-223888400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:223886400-223888400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:223886400-223888400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:223886400-223888800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:223886400-223889000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:223886400-223890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:223886400-223892400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:223886400-223892400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:223886400-223892400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:223886400-223894200	Weak transcription	Brain Angular Gyrus	brain
27	chr1:223886600-223888000	Weak transcription	Ovary	ovary
28	chr1:223886600-223888200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:223886600-223888200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:223886600-223888200	Weak transcription	Fetal Stomach	stomach
31	chr1:223886800-223888800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:223887000-223888200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:223887000-223888400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:223887000-223888400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:223887000-223888400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:223887000-223888400	Enhancers	HSMM	muscle
37	chr1:223887000-223888400	Enhancers	K562	blood
38	chr1:223887000-223888400	Enhancers	Osteobl	bone
39	chr1:223887200-223888000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:223887200-223888200	Enhancers	NH-A	brain
41	chr1:223887200-223888400	Enhancers	HSMMtube	muscle
42	chr1:223887200-223888400	Enhancers	NHLF	lung
43	chr1:223887200-223889400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:223887400-223888600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:223887400-223888600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr1:223887400-223889200	Enhancers	Aorta	Aorta
47	chr1:223887400-223889400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:223887400-223889400	Flanking Active TSS	A549	lung
49	chr1:223887400-223891200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:223887600-223888000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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