Variant report

Variant	rs12506515
Chromosome Location	chr4:78271612-78271613
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78269918..78271823-chr4:78272380..78274841,2	MCF-7	breast:
2	chr4:78270382..78272050-chr4:78274178..78276131,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNI-6	chr4:78271523-78272388	NONHSAT097053

Variant related genes	Relation type
ENSG00000248831	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11930470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11936421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500776	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12501577	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12505837	0.87[AMR][1000 genomes]
rs12506585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511631	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17002580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1806738	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28477195	0.88[ASN][1000 genomes]
rs67295944	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648554	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648563	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72648565	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72648566	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648573	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648578	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72648580	0.82[ASN][1000 genomes]
rs72648581	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72648583	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72648584	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72648585	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72648586	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72650413	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1002683	chr4:78170317-78281331	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1010450	chr4:78182037-78317840	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1004824	chr4:78188691-78312974	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1000447	chr4:78191608-78291173	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3468255	chr4:78237484-78277631	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv5935	chr4:78237568-78277734	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3468256	chr4:78237627-78277552	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1845782	chr4:78237955-78321598	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78269400-78271800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:78269600-78271800	Enhancers	NHDF-Ad	bronchial
3	chr4:78269600-78271800	Enhancers	NHEK	skin
4	chr4:78269800-78272000	Enhancers	HMEC	breast
5	chr4:78270000-78272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:78270000-78273000	Weak transcription	Stomach Mucosa	stomach
7	chr4:78271400-78272000	Enhancers	Fetal Intestine Small	intestine
8	chr4:78271400-78272600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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