Variant report

Variant	rs12898690
Chromosome Location	chr15:40741295-40741296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40741179..40743439-chr15:40758491..40760408,2	K562	blood:
2	chr15:40740139..40742667-chr15:40744605..40747966,4	K562	blood:
3	chr15:40731638..40735002-chr15:40738722..40741318,4	MCF-7	breast:
4	chr15:40741001..40744042-chr15:40747728..40752510,5	K562	blood:

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction
ENSG00000259364	Chromatin interaction
ENSG00000259211	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11853333	0.99[EUR][1000 genomes]
rs62018030	0.80[AMR][1000 genomes]
rs71472440	0.85[EUR][1000 genomes]
rs731640	0.82[AMR][1000 genomes]
rs733299	0.83[AMR][1000 genomes]
rs9972363	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12898690	C15orf57	cis	Esophagus Muscularis	GTEx
rs12898690	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12898690	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12898690	C15orf57	cis	Esophagus Mucosa	GTEx
rs12898690	RP11-111A22.1	cis	lung	GTEx
rs12898690	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12898690	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12898690	KNSTRN	cis	Heart Left Ventricle	GTEx
rs12898690	C15orf57	cis	Artery Tibial	GTEx
rs12898690	C15orf57	cis	lung	GTEx
rs12898690	RP11-111A22.1	cis	Stomach	GTEx
rs12898690	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40734800-40746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:40734800-40747000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:40734800-40751000	Weak transcription	Aorta	Aorta
4	chr15:40735000-40744000	Weak transcription	Primary B cells from cord blood	blood
5	chr15:40735000-40746600	Weak transcription	HSMM	muscle
6	chr15:40735200-40747800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:40735400-40742400	Weak transcription	Psoas Muscle	Psoas
8	chr15:40735600-40743400	Weak transcription	Brain Substantia Nigra	brain
9	chr15:40735800-40742200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:40735800-40743400	Weak transcription	Fetal Thymus	thymus
11	chr15:40735800-40744400	Weak transcription	Hela-S3	cervix
12	chr15:40736000-40742200	Weak transcription	Thymus	Thymus
13	chr15:40736200-40742600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:40736200-40742600	Weak transcription	Dnd41	blood
15	chr15:40736200-40742800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:40736200-40742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:40736200-40743600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:40736200-40743800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:40736400-40742400	Weak transcription	Liver	Liver
20	chr15:40736800-40741400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:40736800-40743400	Weak transcription	Primary T cells from cord blood	blood
22	chr15:40736800-40748600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:40737000-40742000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:40737000-40743400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:40737000-40744400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:40738000-40741400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:40738000-40741400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:40738000-40742400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:40738000-40743600	Weak transcription	Stomach Mucosa	stomach
30	chr15:40738000-40750400	Weak transcription	Brain Germinal Matrix	brain
31	chr15:40738200-40741400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:40738200-40741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:40738200-40741400	Weak transcription	Osteobl	bone
34	chr15:40738200-40742200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:40738200-40742200	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:40738200-40743400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:40738200-40743800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:40738200-40746600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:40738200-40746800	Weak transcription	Adipose Nuclei	Adipose
40	chr15:40738200-40747000	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:40738200-40751000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:40738400-40741400	Weak transcription	NH-A	brain
43	chr15:40738400-40742200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:40738400-40742400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:40738400-40742600	Weak transcription	GM12878-XiMat	blood
46	chr15:40738400-40743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:40738400-40743600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:40738400-40743600	Weak transcription	Right Ventricle	heart
49	chr15:40738400-40744000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:40738400-40744400	Weak transcription	Placenta	Placenta

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