Variant report

Variant	rs1432560
Chromosome Location	chr2:56188956-56188957
allele	A/C
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55945407..55945989-chr2:56188428..56188986,2	MCF-7	breast:
2	chr2:55944515..55947437-chr2:56188349..56191143,2	MCF-7	breast:
3	chr2:56150165..56151052-chr2:56188223..56189072,3	MCF-7	breast:
4	chr2:55945011..55946407-chr2:56188187..56189117,5	K562	blood:
5	chr2:55998494..55999415-chr2:56188226..56189063,2	MCF-7	breast:
6	chr2:55998660..55999310-chr2:56188089..56189086,3	K562	blood:
7	chr2:55958747..55960432-chr2:56187012..56189326,2	K562	blood:
8	chr12:2903788..2906211-chr2:56187891..56190669,2	MCF-7	breast:
9	chr2:56187210..56190071-chr2:56191391..56193290,2	K562	blood:
10	chr2:56149371..56151100-chr2:56187829..56189531,2	MCF-7	breast:
11	chr2:55998188..55999614-chr2:56188128..56189121,13	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-1	chr2:56186575-56191017	NONHSAT070812

No data

Variant related genes	Relation type
ENSG00000004478	Chromatin interaction
ENSG00000115380	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10185077	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10192259	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125611	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472832	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13431149	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432563	0.98[ASN][1000 genomes]
rs1432564	0.97[ASN][1000 genomes]
rs1465685	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1583266	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1583267	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1897478	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278366	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868984	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34552760	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3972318	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453721	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4635565	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672080	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672081	0.98[ASN][1000 genomes]
rs4672082	0.98[ASN][1000 genomes]
rs55805406	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545531	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704991	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721145	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6724998	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733881	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733889	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6747490	0.99[ASN][1000 genomes]
rs724539	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724540	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7422809	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7561395	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561417	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7564964	0.98[ASN][1000 genomes]
rs981037	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56186400-56193200	Weak transcription	NH-A	brain
2	chr2:56186600-56189000	Weak transcription	HSMMtube	muscle
3	chr2:56187800-56189200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:56188000-56189800	Enhancers	HUVEC	blood vessel
5	chr2:56188000-56190800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:56188200-56189200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:56188200-56189200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:56188200-56189200	Enhancers	A549	lung
9	chr2:56188400-56189000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:56188400-56189000	Enhancers	HMEC	breast
11	chr2:56188400-56189000	Enhancers	HSMM	muscle
12	chr2:56188400-56189200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:56188400-56189200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:56188400-56189200	Enhancers	Osteobl	bone
15	chr2:56188600-56189200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:56188600-56192600	Weak transcription	Adipose Nuclei	Adipose
17	chr2:56188800-56189200	Enhancers	Colon Smooth Muscle	Colon
18	chr2:56188800-56193000	Weak transcription	Fetal Lung	lung

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