Variant report

Variant	rs7412088
Chromosome Location	chr1:223899123-223899124
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223899071-223899271	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:223898974-223899311	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:223898978-223899311	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:223898971-223899240	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:223898708-223906948	U87	brain:	n/a	n/a
6	POLR2A	chr1:223898865-223899304	U87	brain:	n/a	n/a
7	FOS	chr1:223898982-223899305	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:223898702-223906954	U87	brain:	n/a	n/a
9	E2F4	chr1:223898924-223899230	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:223898997-223899308	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:223898969-223899308	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr1:223899030-223899214	MCF10A-Er-Src	breast:	n/a	n/a
13	GATA3	chr1:223898813-223899234	T-47D	breast:	n/a	n/a
14	POLR2A	chr1:223898874-223899304	U87	brain:	n/a	n/a
15	STAT3	chr1:223898977-223899309	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr1:223898981-223899323	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223886668..223890344-chr1:223897746..223900327,3	K562	blood:
2	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
3	chr1:223882393..223884567-chr1:223898139..223900023,2	MCF-7	breast:
4	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
5	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
6	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
7	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000143514	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10799550	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916600	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916601	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916602	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916634	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10916646	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11580460	0.95[EUR][1000 genomes]
rs12066704	0.86[CEU][hapmap]
rs12069561	0.86[CEU][hapmap]
rs12070364	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12074091	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1222138	0.86[CEU][hapmap]
rs1222141	0.87[CEU][hapmap]
rs12567519	0.80[EUR][1000 genomes]
rs12568612	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1419305	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1539707	0.92[EUR][1000 genomes]
rs17556570	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs17598	0.86[CEU][hapmap]
rs1779658	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1892076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892077	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2040103	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2186006	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28370014	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28739569	0.95[EUR][1000 genomes]
rs2896828	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3738373	0.86[CEU][hapmap]
rs3738374	0.86[CEU][hapmap]
rs4233224	0.82[ASN][1000 genomes]
rs4511081	0.86[EUR][1000 genomes]
rs4653499	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4653500	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653522	0.86[CEU][hapmap]
rs4653834	0.89[ASN][1000 genomes]
rs61822636	0.80[EUR][1000 genomes]
rs61823962	0.83[EUR][1000 genomes]
rs61823965	0.86[EUR][1000 genomes]
rs61823966	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61823967	0.97[EUR][1000 genomes]
rs61823968	0.97[EUR][1000 genomes]
rs61823980	0.95[EUR][1000 genomes]
rs61823981	0.95[EUR][1000 genomes]
rs6669046	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6669080	0.82[CEU][hapmap]
rs6674492	0.81[CHB][hapmap]
rs6674733	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6683379	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6702314	0.85[EUR][1000 genomes]
rs6702430	0.84[EUR][1000 genomes]
rs6703104	0.86[CEU][hapmap]
rs7414311	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751609	0.87[CEU][hapmap]
rs7517684	0.93[EUR][1000 genomes]
rs7524132	0.85[ASN][1000 genomes]
rs7525446	0.95[EUR][1000 genomes]
rs7539624	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7543197	1.00[CEU][hapmap]
rs7547642	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7554857	0.89[ASN][1000 genomes]
rs7555491	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][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
rs7412088	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223892200-223899800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:223893400-223899600	Weak transcription	Fetal Kidney	kidney
4	chr1:223894000-223899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:223894000-223899800	Enhancers	Fetal Intestine Large	intestine
6	chr1:223895400-223899400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:223895600-223899400	Weak transcription	Esophagus	oesophagus
8	chr1:223895600-223899600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223895600-223899600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:223895600-223899800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:223895800-223899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:223895800-223899600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:223895800-223899600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:223895800-223899600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:223895800-223899600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:223895800-223899600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:223895800-223899600	Weak transcription	Right Ventricle	heart
18	chr1:223895800-223899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:223896000-223899400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:223896000-223899400	Weak transcription	Pancreas	Pancrea
21	chr1:223896000-223899600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:223896000-223899600	Weak transcription	Aorta	Aorta
23	chr1:223896000-223899600	Weak transcription	Colonic Mucosa	Colon
24	chr1:223896000-223899600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:223896000-223899600	Weak transcription	Ovary	ovary
26	chr1:223896000-223899800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:223896000-223899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:223896000-223899800	Weak transcription	Left Ventricle	heart
29	chr1:223896000-223899800	Weak transcription	Psoas Muscle	Psoas
30	chr1:223896000-223900000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:223896000-223900200	Weak transcription	Small Intestine	intestine
32	chr1:223896200-223899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:223896800-223899800	Weak transcription	Placenta	Placenta
34	chr1:223897000-223899200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:223897000-223899400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:223897000-223899600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:223897000-223899600	Weak transcription	HSMM	muscle
38	chr1:223897000-223899600	Weak transcription	HSMMtube	muscle
39	chr1:223897200-223900000	Weak transcription	Lung	lung
40	chr1:223897600-223899800	Enhancers	Fetal Intestine Small	intestine
41	chr1:223897600-223899800	Enhancers	Fetal Lung	lung
42	chr1:223897600-223900200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:223898000-223899600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:223898200-223899400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:223898200-223899600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr1:223898200-223899600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:223898400-223899600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr1:223898400-223899800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:223898600-223899400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:223898600-223899400	Enhancers	Primary T helper cells PMA-I stimulated	--

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