Variant report

Variant	rs7547642
Chromosome Location	chr1:223921480-223921481
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223919205..223921124-chr1:223921422..223926352,4	K562	blood:
2	chr1:223903451..223905300-chr1:223920938..223923297,2	MCF-7	breast:
3	chr1:223907868..223910844-chr1:223920862..223922625,2	K562	blood:
4	chr1:223892791..223896772-chr1:223919510..223922888,4	MCF-7	breast:
5	chr1:223914702..223917591-chr1:223920131..223923452,6	K562	blood:
6	chr1:223919304..223920937-chr1:223921422..223924041,2	K562	blood:
7	chr1:223918635..223922245-chr1:223925850..223929641,4	MCF-7	breast:
8	chr1:223907966..223910136-chr1:223920421..223923104,3	K562	blood:
9	chr1:223914562..223916498-chr1:223920143..223922062,2	K562	blood:
10	chr1:223897765..223900392-chr1:223919189..223921724,2	MCF-7	breast:
11	chr1:223898782..223903083-chr1:223918027..223924082,6	K562	blood:
12	chr1:223913054..223915038-chr1:223921368..223922985,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10799550	0.82[EUR][1000 genomes]
rs10916600	0.93[EUR][1000 genomes]
rs10916601	0.92[EUR][1000 genomes]
rs10916602	0.92[EUR][1000 genomes]
rs10916603	0.93[EUR][1000 genomes]
rs10916634	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10916646	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11580460	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588475	0.90[ASN][1000 genomes]
rs12066704	0.87[CEU][hapmap]
rs12069561	0.87[CEU][hapmap]
rs12070364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12074091	0.92[EUR][1000 genomes]
rs1222138	0.87[CEU][hapmap]
rs1222141	0.87[CEU][hapmap]
rs12568612	0.87[CEU][hapmap]
rs1419305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539707	0.91[EUR][1000 genomes]
rs17556570	0.87[CEU][hapmap]
rs17598	0.87[CEU][hapmap]
rs1779658	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1892076	0.93[EUR][1000 genomes]
rs1892077	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2186006	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs28370014	0.91[EUR][1000 genomes]
rs28739569	0.90[EUR][1000 genomes]
rs3738373	0.87[CEU][hapmap]
rs3738374	0.87[CEU][hapmap]
rs4511081	0.81[EUR][1000 genomes]
rs4653499	0.92[EUR][1000 genomes]
rs4653500	0.93[EUR][1000 genomes]
rs4653522	0.87[CEU][hapmap]
rs61823965	0.81[EUR][1000 genomes]
rs61823966	0.92[EUR][1000 genomes]
rs61823967	0.92[EUR][1000 genomes]
rs61823968	0.92[EUR][1000 genomes]
rs61823980	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61823981	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669046	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6669080	0.82[CEU][hapmap]
rs6674733	0.94[EUR][1000 genomes]
rs6702314	0.80[EUR][1000 genomes]
rs6703104	0.87[CEU][hapmap]
rs7412088	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7414311	0.92[EUR][1000 genomes]
rs751609	0.87[CEU][hapmap]
rs7517684	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525446	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7543197	1.00[CEU][hapmap]
rs7555491	1.00[CEU][hapmap];0.92[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
rs7547642	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr1:223914400-223921800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:223915400-223927200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:223916600-223927000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
12	chr1:223916800-223922400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:223917000-223922200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:223917800-223921800	Enhancers	Brain Angular Gyrus	brain
15	chr1:223917800-223922200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:223917800-223922400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:223917800-223922600	Enhancers	Fetal Lung	lung
18	chr1:223917800-223922800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:223918000-223921600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:223918200-223922000	Enhancers	Brain Substantia Nigra	brain
21	chr1:223918200-223923000	Enhancers	Stomach Mucosa	stomach
22	chr1:223918400-223921600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr1:223918400-223921600	Enhancers	Right Ventricle	heart
24	chr1:223918400-223921800	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr1:223918400-223921800	Enhancers	Colon Smooth Muscle	Colon
26	chr1:223918400-223921800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:223918400-223921800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:223918400-223922000	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:223918400-223922400	Enhancers	Left Ventricle	heart
30	chr1:223918400-223922400	Enhancers	Small Intestine	intestine
31	chr1:223918400-223922800	Enhancers	Fetal Heart	heart
32	chr1:223918400-223924000	Enhancers	Right Atrium	heart
33	chr1:223918600-223922600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:223918600-223922600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:223918800-223921800	Genic enhancers	Esophagus	oesophagus
36	chr1:223918800-223922200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr1:223918800-223922800	Genic enhancers	Fetal Stomach	stomach
38	chr1:223919000-223922200	Enhancers	Fetal Kidney	kidney
39	chr1:223919200-223921600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:223919200-223922000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:223919400-223921600	Genic enhancers	Osteobl	bone
44	chr1:223919400-223922400	Genic enhancers	NHDF-Ad	bronchial
45	chr1:223919400-223923000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:223919400-223923200	Strong transcription	Hela-S3	cervix
47	chr1:223919600-223921600	Enhancers	Adipose Nuclei	Adipose
48	chr1:223919600-223921600	Enhancers	HUVEC	blood vessel
49	chr1:223919600-223922200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:223919600-223922400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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