Variant report

Variant	rs825126
Chromosome Location	chr1:223493373-223493374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223473310..223474999-chr1:223493022..223494928,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1341288	1.00[EUR][1000 genomes]
rs1417744	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1640803	1.00[MEX][hapmap]
rs1713218	1.00[ASW][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs17518279	0.80[YRI][hapmap]
rs1856932	1.00[EUR][1000 genomes]
rs2253649	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs2487832	1.00[EUR][1000 genomes]
rs2793466	1.00[EUR][1000 genomes]
rs28584917	1.00[EUR][1000 genomes]
rs3768284	1.00[MEX][hapmap]
rs5744122	1.00[MEX][hapmap]
rs73122236	1.00[EUR][1000 genomes]
rs73122238	1.00[EUR][1000 genomes]
rs73122239	1.00[EUR][1000 genomes]
rs825119	1.00[EUR][1000 genomes]
rs825121	1.00[EUR][1000 genomes]
rs825122	1.00[EUR][1000 genomes]
rs851140	1.00[MEX][hapmap]
rs851151	1.00[MEX][hapmap]
rs851195	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs851197	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs851200	0.89[ASW][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs825126	CAPN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223487200-223496000	Weak transcription	Ovary	ovary
2	chr1:223489800-223494000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:223489800-223495600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:223492200-223497000	Weak transcription	Right Atrium	heart
5	chr1:223492400-223496200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:223492800-223493400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223492800-223493400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:223492800-223493400	Enhancers	HMEC	breast
9	chr1:223492800-223493400	Enhancers	NHEK	skin
10	chr1:223492800-223493600	Enhancers	Fetal Lung	lung
11	chr1:223492800-223494200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:223492800-223494200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:223492800-223494200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:223492800-223494600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:223492800-223494800	Enhancers	Fetal Thymus	thymus
16	chr1:223493000-223493400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:223493000-223494200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:223493000-223494400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:223493200-223493400	Enhancers	Pancreas	Pancrea
20	chr1:223493200-223493600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:223493200-223493600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:223493200-223493600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:223493200-223493800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:223493200-223493800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:223493200-223494200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:223493200-223494200	Enhancers	Thymus	Thymus
27	chr1:223493200-223494600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:223493200-223494600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:223493200-223494600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:223493200-223494600	Enhancers	Esophagus	oesophagus

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