Variant report

Variant	rs7549063
Chromosome Location	chr1:223909826-223909827
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	chr1:223907922..223910776-chr1:223912986..223915507,4	MCF-7	breast:
2	chr1:223889991..223892521-chr1:223908997..223911064,2	K562	blood:
3	chr1:223907382..223910369-chr1:223910890..223914136,6	MCF-7	breast:
4	chr1:223907868..223910844-chr1:223920862..223922625,2	K562	blood:
5	chr1:223907966..223910136-chr1:223920421..223923104,3	K562	blood:
6	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
7	chr1:223893339..223895149-chr1:223908557..223910552,2	K562	blood:
8	chr1:223908483..223912094-chr1:223930572..223933646,3	MCF-7	breast:
9	chr1:223907649..223910322-chr1:223936946..223940552,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503144	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10915702	0.81[EUR][1000 genomes]
rs12059770	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12066704	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12066829	0.81[EUR][1000 genomes]
rs12066831	0.81[EUR][1000 genomes]
rs12069561	0.85[CEU][hapmap]
rs12070057	0.81[EUR][1000 genomes]
rs12080250	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12088254	1.00[CEU][hapmap]
rs1222138	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1222140	0.84[EUR][1000 genomes]
rs1222141	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1222142	0.83[EUR][1000 genomes]
rs12563291	0.83[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12563713	0.82[EUR][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12566817	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12568612	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[JPT][hapmap]
rs16842162	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842257	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842326	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842343	1.00[JPT][hapmap]
rs17556570	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597	0.83[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap]
rs28370026	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370043	0.99[EUR][1000 genomes]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap]
rs4653522	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4993742	0.82[CEU][hapmap]
rs59248553	0.81[EUR][1000 genomes]
rs59275322	0.84[EUR][1000 genomes]
rs61823964	0.83[EUR][1000 genomes]
rs61823979	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6671245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678365	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6683052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685557	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6691315	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693884	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6696053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6700366	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6703104	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7331	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs751609	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7530328	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7533551	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7535882	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7555226	0.84[EUR][1000 genomes]
rs898876	0.81[EUR][1000 genomes]
rs898877	0.80[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
rs7549063	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
7	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:223904400-223922400	Genic enhancers	NHLF	lung
10	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
11	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
12	chr1:223904800-223910600	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr1:223904800-223911800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
15	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr1:223905000-223911600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:223905200-223911400	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:223905600-223910800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:223905600-223910800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:223905600-223912200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:223905600-223912400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:223906000-223913800	Weak transcription	Primary B cells from cord blood	blood
23	chr1:223906200-223913000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:223906200-223915600	Weak transcription	Aorta	Aorta
25	chr1:223906400-223910800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:223906400-223913600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:223906400-223913600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:223906600-223913800	Weak transcription	Fetal Thymus	thymus
29	chr1:223906600-223921000	Weak transcription	Fetal Brain Male	brain
30	chr1:223907400-223913200	Weak transcription	K562	blood
31	chr1:223907600-223910200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:223907600-223912200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:223907600-223913400	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:223907800-223913200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:223907800-223913600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:223907800-223913600	Weak transcription	Fetal Heart	heart
37	chr1:223907800-223913800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:223908400-223910000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:223908400-223912200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:223908400-223913600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:223908600-223910200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr1:223908600-223910200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:223908600-223910600	Strong transcription	Fetal Lung	lung
44	chr1:223908600-223911600	Genic enhancers	NHEK	skin
45	chr1:223908600-223911800	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr1:223908800-223910000	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr1:223908800-223910600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:223908800-223913400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:223908800-223913600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:223909000-223911400	Genic enhancers	Lung	lung

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