Variant report

Variant	rs4653499
Chromosome Location	chr1:223892703-223892704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223891679..223894044-chr1:223943117..223944759,2	MCF-7	breast:
2	chr1:223887828..223890332-chr1:223892364..223895816,5	K562	blood:
3	chr1:223853261..223855880-chr1:223892396..223895154,2	MCF-7	breast:
4	chr1:223890524..223893483-chr1:223939382..223941203,2	MCF-7	breast:
5	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
6	chr1:223891592..223893967-chr1:223903233..223904840,2	K562	blood:
7	chr1:223891793..223894789-chr1:224032613..224034264,2	K562	blood:
8	chr1:223891739..223894033-chr1:224033378..224035104,2	K562	blood:
9	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10799550	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10916600	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916601	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916602	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916603	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916604	0.88[ASN][1000 genomes]
rs10916634	0.94[EUR][1000 genomes]
rs10916646	0.94[EUR][1000 genomes]
rs11579787	0.82[ASN][1000 genomes]
rs11580460	0.94[EUR][1000 genomes]
rs11580689	0.82[ASN][1000 genomes]
rs11581716	0.82[ASN][1000 genomes]
rs12057708	0.88[ASN][1000 genomes]
rs12070364	0.94[EUR][1000 genomes]
rs12074091	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080565	0.95[ASN][1000 genomes]
rs12567519	0.81[EUR][1000 genomes]
rs12568612	0.81[EUR][1000 genomes]
rs1419305	0.94[EUR][1000 genomes]
rs1539707	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16842040	0.93[ASN][1000 genomes]
rs16842062	0.82[ASN][1000 genomes]
rs17556570	0.81[EUR][1000 genomes]
rs1779658	0.89[EUR][1000 genomes]
rs1892076	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1892077	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000320	0.88[ASN][1000 genomes]
rs2154113	0.96[ASN][1000 genomes]
rs2186006	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275877	0.96[ASN][1000 genomes]
rs28370012	0.96[ASN][1000 genomes]
rs28370013	0.96[ASN][1000 genomes]
rs28370014	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370020	0.96[ASN][1000 genomes]
rs28370029	0.80[ASN][1000 genomes]
rs28739569	0.96[EUR][1000 genomes]
rs4511081	0.87[EUR][1000 genomes]
rs4653500	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61822636	0.81[EUR][1000 genomes]
rs61823962	0.84[EUR][1000 genomes]
rs61823965	0.87[EUR][1000 genomes]
rs61823966	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823967	0.98[EUR][1000 genomes]
rs61823968	0.98[EUR][1000 genomes]
rs61823980	0.94[EUR][1000 genomes]
rs61823981	0.94[EUR][1000 genomes]
rs6669046	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6674733	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702314	0.86[EUR][1000 genomes]
rs6702430	0.85[EUR][1000 genomes]
rs7366009	0.96[ASN][1000 genomes]
rs7412088	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7414311	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517684	0.92[EUR][1000 genomes]
rs7525446	0.94[EUR][1000 genomes]
rs7547642	0.92[EUR][1000 genomes]
rs7555491	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs4653499	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223886400-223894200	Weak transcription	Brain Angular Gyrus	brain
2	chr1:223888200-223892800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:223889000-223894000	Weak transcription	Pancreas	Pancrea
4	chr1:223889000-223895000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:223889000-223895400	Enhancers	NHLF	lung
6	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:223889200-223892800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:223889200-223893200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:223889400-223892800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:223889400-223892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:223889400-223893200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:223889400-223893600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:223889400-223894000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:223891000-223895200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:223891000-223895400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:223891200-223898600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:223891400-223892800	Enhancers	A549	lung
18	chr1:223891600-223893400	Weak transcription	Hela-S3	cervix
19	chr1:223891800-223892800	Enhancers	Fetal Heart	heart
20	chr1:223892000-223892800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:223892000-223894000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:223892000-223894000	Enhancers	NH-A	brain
23	chr1:223892000-223895000	Enhancers	NHDF-Ad	bronchial
24	chr1:223892000-223897000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:223892200-223892800	Enhancers	Esophagus	oesophagus
26	chr1:223892200-223893000	Enhancers	Right Atrium	heart
27	chr1:223892200-223893400	Enhancers	Spleen	Spleen
28	chr1:223892200-223893600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:223892200-223894000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:223892200-223894200	Enhancers	HSMMtube	muscle
31	chr1:223892200-223894600	Enhancers	Ovary	ovary
32	chr1:223892200-223895000	Enhancers	K562	blood
33	chr1:223892200-223895200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:223892200-223895600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:223892200-223895800	Enhancers	Fetal Lung	lung
36	chr1:223892200-223895800	Enhancers	Right Ventricle	heart
37	chr1:223892200-223896000	Enhancers	Left Ventricle	heart
38	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:223892400-223892800	Enhancers	Brain Hippocampus Middle	brain
40	chr1:223892400-223893200	Weak transcription	Gastric	stomach
41	chr1:223892400-223893200	Enhancers	Lung	lung
42	chr1:223892400-223893200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr1:223892400-223893400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:223892400-223893400	Enhancers	Fetal Kidney	kidney
45	chr1:223892400-223893600	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:223892400-223894600	Enhancers	Fetal Brain Male	brain
47	chr1:223892400-223895200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:223892400-223895200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:223892400-223895200	Enhancers	HMEC	breast
50	chr1:223892400-223895200	Enhancers	HUVEC	blood vessel

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