Variant report

Variant	rs12899910
Chromosome Location	chr15:41125011-41125012
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41124557..41126932-chr15:41129438..41132345,2	K562	blood:
2	chr15:41100215..41102460-chr15:41122818..41125777,2	K562	blood:
3	chr15:41119625..41122086-chr15:41123755..41126786,3	K562	blood:
4	chr15:41115426..41119374-chr15:41121588..41125494,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166140	Chromatin interaction
ENSG00000166143	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11070294	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070295	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070296	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070297	0.81[ASN][1000 genomes]
rs11856866	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12148058	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905621	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909824	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12911376	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12916485	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17657877	0.81[EUR][1000 genomes]
rs17657986	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34143869	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34948298	0.89[EUR][1000 genomes]
rs35458726	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35621205	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35853942	0.80[EUR][1000 genomes]
rs3736286	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3743033	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743034	0.83[ASN][1000 genomes]
rs4402538	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57994257	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6492967	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs745032	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036842	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037830	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12899910	ZFYVE19	cis	Artery Tibial	GTEx
rs12899910	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs12899910	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12899910	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12899910	C15orf57	cis	Artery Tibial	GTEx
rs12899910	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12899910	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41107200-41135200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41107600-41135200	Weak transcription	Esophagus	oesophagus
3	chr15:41108200-41135600	Weak transcription	Spleen	Spleen
4	chr15:41112000-41135800	Weak transcription	Right Atrium	heart
5	chr15:41119200-41126800	Weak transcription	Hela-S3	cervix
6	chr15:41120800-41135600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:41121600-41129800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:41121600-41135200	Weak transcription	Colonic Mucosa	Colon
9	chr15:41121600-41135200	Weak transcription	Gastric	stomach
10	chr15:41121600-41135200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:41121800-41135200	Weak transcription	Stomach Mucosa	stomach
12	chr15:41122200-41126600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:41122800-41135000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:41123200-41135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:41123400-41125200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:41123600-41135000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:41124000-41127400	Enhancers	Placenta	Placenta
18	chr15:41124800-41127800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:41124800-41128200	Weak transcription	Fetal Intestine Small	intestine
20	chr15:41124800-41135200	Weak transcription	Pancreas	Pancrea

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