Variant report

Variant	rs12898459
Chromosome Location	chr15:42329119-42329120
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	chr15:42313009..42314884-chr15:42328123..42329860,2	K562	blood:
2	chr15:42326664..42329520-chr15:42335867..42337408,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11638234	0.82[ASN][1000 genomes]
rs12901016	0.80[ASN][1000 genomes]
rs12904287	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12914009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1823552	0.89[AFR][1000 genomes]
rs2598466	0.87[AFR][1000 genomes]
rs2665208	0.87[EUR][1000 genomes]
rs2665211	0.88[AFR][1000 genomes]
rs4924606	0.84[EUR][1000 genomes]
rs6493019	0.91[EUR][1000 genomes]
rs7165532	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7166079	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv904130	chr15:42323591-42336018	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42326200-42337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:42327000-42329400	Enhancers	Primary B cells from peripheral blood	blood
3	chr15:42327600-42330000	Weak transcription	Pancreas	Pancrea
4	chr15:42327800-42329200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:42327800-42329200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:42327800-42329600	Weak transcription	Lung	lung
7	chr15:42327800-42330000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:42327800-42331000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42328000-42329200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:42328000-42329200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:42328000-42329400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:42328000-42329600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:42328000-42329800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:42328000-42330800	Enhancers	HMEC	breast
15	chr15:42328000-42337400	Weak transcription	Fetal Intestine Small	intestine
16	chr15:42328200-42329600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:42328600-42329400	Weak transcription	Colonic Mucosa	Colon
18	chr15:42328600-42329600	Weak transcription	NHEK	skin
19	chr15:42328600-42329800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:42328800-42329800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:42328800-42330400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:42329000-42331000	Enhancers	Esophagus	oesophagus
23	chr15:42329000-42333600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:42329000-42335400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:42329000-42336600	Weak transcription	Spleen	Spleen

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