Variant report

Variant	rs7525446
Chromosome Location	chr1:223914453-223914454
allele	C/T
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	chr1:223898332..223906168-chr1:223910455..223917097,17	K562	blood:
2	chr1:223913291..223915988-chr1:223981454..223983055,2	K562	blood:
3	chr1:223899168..223900850-chr1:223913497..223916272,3	MCF-7	breast:
4	chr1:223907922..223910776-chr1:223912986..223915507,4	MCF-7	breast:
5	chr1:223913473..223915896-chr1:224022022..224024045,2	K562	blood:
6	chr1:223913054..223915038-chr1:223921368..223922985,2	MCF-7	breast:
7	chr1:223889048..223892009-chr1:223912186..223915983,3	K562	blood:
8	chr1:223914360..223914989-chr12:65959195..65960066,2	MCF-7	breast:
9	chr1:223893369..223895448-chr1:223913219..223916092,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10799550	0.84[EUR][1000 genomes]
rs10916600	0.95[EUR][1000 genomes]
rs10916601	0.94[EUR][1000 genomes]
rs10916602	0.94[EUR][1000 genomes]
rs10916603	0.95[EUR][1000 genomes]
rs10916634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580460	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070364	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12074091	0.94[EUR][1000 genomes]
rs1419305	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1539707	0.93[EUR][1000 genomes]
rs1779658	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1892076	0.95[EUR][1000 genomes]
rs1892077	0.94[EUR][1000 genomes]
rs2186006	0.94[EUR][1000 genomes]
rs28370014	0.93[EUR][1000 genomes]
rs28739569	0.92[EUR][1000 genomes]
rs4511081	0.83[EUR][1000 genomes]
rs4653499	0.94[EUR][1000 genomes]
rs4653500	0.95[EUR][1000 genomes]
rs61823962	0.80[EUR][1000 genomes]
rs61823965	0.83[EUR][1000 genomes]
rs61823966	0.94[EUR][1000 genomes]
rs61823967	0.94[EUR][1000 genomes]
rs61823968	0.94[EUR][1000 genomes]
rs61823980	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61823981	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669046	0.96[EUR][1000 genomes]
rs6674733	0.96[EUR][1000 genomes]
rs6702314	0.82[EUR][1000 genomes]
rs6702430	0.81[EUR][1000 genomes]
rs7412088	0.95[EUR][1000 genomes]
rs7414311	0.94[EUR][1000 genomes]
rs7517684	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7547642	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7555491	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7525446	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:223904400-223922400	Genic enhancers	NHLF	lung
3	chr1:223906200-223915600	Weak transcription	Aorta	Aorta
4	chr1:223906600-223921000	Weak transcription	Fetal Brain Male	brain
5	chr1:223910400-223914600	Genic enhancers	NH-A	brain
6	chr1:223910800-223915600	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr1:223910800-223916400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:223910800-223916800	Genic enhancers	Gastric	stomach
9	chr1:223910800-223919800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:223911600-223915800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:223911800-223917200	Genic enhancers	Muscle Satellite Cultured Cells	--
12	chr1:223912600-223916000	Genic enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:223913000-223914600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:223913000-223914600	Enhancers	HUVEC	blood vessel
15	chr1:223913000-223916600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:223913200-223914800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
17	chr1:223913200-223915000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:223913200-223915200	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:223913200-223915200	Enhancers	Small Intestine	intestine
20	chr1:223913200-223915400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:223913200-223915400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:223913200-223915600	Genic enhancers	Fetal Stomach	stomach
23	chr1:223913200-223916000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:223913200-223916200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:223913200-223916200	Enhancers	Left Ventricle	heart
26	chr1:223913400-223914600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr1:223913400-223914800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:223913400-223915000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:223913400-223915000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:223913400-223915200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:223913400-223915200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:223913400-223915200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:223913400-223915200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:223913400-223915200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:223913400-223915200	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:223913400-223915600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:223913400-223915600	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:223913400-223915600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:223913400-223915600	Enhancers	Lung	lung
40	chr1:223913400-223915800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr1:223913400-223915800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:223913400-223915800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr1:223913400-223915800	Enhancers	Placenta	Placenta
44	chr1:223913400-223915800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:223913400-223915800	Genic enhancers	HSMM	muscle
46	chr1:223913400-223916000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:223913400-223916000	Enhancers	Right Atrium	heart
48	chr1:223913400-223916400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:223913400-223916400	Enhancers	Spleen	Spleen
50	chr1:223913600-223914600	Enhancers	Psoas Muscle	Psoas

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