Variant report

Variant	rs12903887
Chromosome Location	chr15:58562231-58562232
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58560557..58563297-chr15:59039690..59042665,2	MCF-7	breast:
2	chr15:58559923..58562292-chr15:58623046..58626671,3	K562	blood:
3	chr15:58553979..58557970-chr15:58560575..58563562,3	K562	blood:
4	chr15:58555185..58557970-chr15:58559475..58563925,5	K562	blood:
5	chr15:58559736..58562598-chr15:58575137..58576771,2	K562	blood:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12906488	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12914167	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34233191	0.82[EUR][1000 genomes]
rs34436673	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35440059	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35525462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35768119	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59220434	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60276704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71478654	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71478656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71478657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71478658	0.87[EUR][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	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1050473	chr15:58479888-58562270	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv904264	chr15:58505122-58588510	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv904265	chr15:58517528-58588510	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58553400-58562400	Weak transcription	Spleen	Spleen
2	chr15:58554200-58574400	Weak transcription	Left Ventricle	heart
3	chr15:58557400-58562400	Weak transcription	Dnd41	blood
4	chr15:58559000-58562400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:58559000-58562600	Enhancers	Hela-S3	cervix
6	chr15:58559200-58562800	Enhancers	Placenta	Placenta
7	chr15:58559800-58562400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:58560400-58562800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:58560600-58562600	Enhancers	Thymus	Thymus
10	chr15:58561000-58562600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:58561000-58562600	Enhancers	GM12878-XiMat	blood
12	chr15:58561200-58562600	Enhancers	HMEC	breast
13	chr15:58561200-58562800	Enhancers	Fetal Thymus	thymus
14	chr15:58561400-58562400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:58561400-58562600	Enhancers	Primary T cells from cord blood	blood
16	chr15:58561400-58562600	Enhancers	Brain Anterior Caudate	brain
17	chr15:58561600-58562800	Enhancers	Fetal Intestine Large	intestine
18	chr15:58561800-58562600	Enhancers	Brain Hippocampus Middle	brain
19	chr15:58561800-58562600	Enhancers	Brain Substantia Nigra	brain
20	chr15:58561800-58562800	Enhancers	Liver	Liver
21	chr15:58561800-58562800	Enhancers	Fetal Intestine Small	intestine
22	chr15:58561800-58562800	Enhancers	Stomach Mucosa	stomach
23	chr15:58561800-58563000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr15:58562000-58562600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr15:58562000-58562600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr15:58562000-58562600	Enhancers	Fetal Muscle Trunk	muscle
27	chr15:58562000-58562600	Enhancers	HSMM	muscle
28	chr15:58562000-58562800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr15:58562000-58562800	Enhancers	A549	lung
30	chr15:58562000-58562800	Enhancers	HepG2	liver
31	chr15:58562200-58562400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:58562200-58562600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr15:58562200-58562800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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