Variant report

Variant	rs12593739
Chromosome Location	chr15:41252202-41252203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41196325..41199038-chr15:41249965..41253557,4	K562	blood:
2	chr15:41251504..41254732-chr15:41263210..41265996,3	K562	blood:
3	chr15:41221931..41225050-chr15:41249351..41252849,3	K562	blood:
4	chr15:41212940..41214641-chr15:41251110..41253337,2	K562	blood:
5	chr15:41224639..41226841-chr15:41251663..41253494,2	MCF-7	breast:
6	chr15:41220599..41223039-chr15:41251392..41253902,3	MCF-7	breast:
7	chr15:41195848..41199038-chr15:41251277..41253557,3	K562	blood:

Variant related genes	Relation type
ENSG00000128917	Chromatin interaction
ENSG00000251161	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001341	0.87[EUR][1000 genomes]
rs10851400	0.92[ASN][1000 genomes]
rs11070313	0.83[ASN][1000 genomes]
rs11070314	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070315	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11557249	0.90[ASN][1000 genomes]
rs11853377	0.90[ASN][1000 genomes]
rs11854054	0.89[ASN][1000 genomes]
rs11855248	0.83[EUR][1000 genomes]
rs11857572	0.89[ASN][1000 genomes]
rs12899590	0.84[EUR][1000 genomes]
rs12905926	0.80[EUR][1000 genomes]
rs12910027	0.80[EUR][1000 genomes]
rs1869907	0.91[EUR][1000 genomes]
rs2412572	0.85[EUR][1000 genomes]
rs2412574	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28479904	0.84[EUR][1000 genomes]
rs28501589	0.82[EUR][1000 genomes]
rs28538500	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28572344	0.81[EUR][1000 genomes]
rs28575174	0.90[ASN][1000 genomes]
rs2899002	0.93[EUR][1000 genomes]
rs3900905	0.87[EUR][1000 genomes]
rs3986311	0.87[EUR][1000 genomes]
rs4244584	0.86[EUR][1000 genomes]
rs4497658	0.88[EUR][1000 genomes]
rs4923890	0.88[EUR][1000 genomes]
rs4924519	0.87[EUR][1000 genomes]
rs4924520	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924521	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924522	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924523	0.96[EUR][1000 genomes]
rs4924524	0.96[EUR][1000 genomes]
rs4924525	0.89[EUR][1000 genomes]
rs4924526	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924528	0.91[EUR][1000 genomes]
rs60588038	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162992	0.80[EUR][1000 genomes]
rs7169669	0.81[EUR][1000 genomes]
rs7174555	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72735675	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs745299	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8030306	0.89[EUR][1000 genomes]
rs8042127	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042230	0.87[ASN][1000 genomes]
rs9796	0.82[EUR][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	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
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv1794127	chr15:41245289-41276158	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12593739	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41246400-41268200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41246600-41252400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41246600-41252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:41246600-41253400	Enhancers	Fetal Muscle Leg	muscle
5	chr15:41246600-41258200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:41246600-41270000	Weak transcription	HUVEC	blood vessel
7	chr15:41246800-41253000	Weak transcription	A549	lung
8	chr15:41246800-41268000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:41246800-41268200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:41247400-41253600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41248400-41254200	Weak transcription	Osteobl	bone
12	chr15:41249000-41258400	Weak transcription	K562	blood
13	chr15:41249200-41252800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:41249400-41266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:41249400-41268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:41249600-41258600	Weak transcription	NHLF	lung
17	chr15:41250000-41252400	Weak transcription	Lung	lung
18	chr15:41250000-41258400	Weak transcription	Right Atrium	heart
19	chr15:41250000-41264400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:41250200-41252600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:41250200-41253400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:41250200-41255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:41250400-41252400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:41250400-41252600	Weak transcription	Colonic Mucosa	Colon
25	chr15:41250600-41252400	Weak transcription	Stomach Mucosa	stomach
26	chr15:41250600-41252600	Weak transcription	Right Ventricle	heart
27	chr15:41250600-41252800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:41250600-41253000	Weak transcription	Esophagus	oesophagus
29	chr15:41250600-41258200	Weak transcription	Left Ventricle	heart
30	chr15:41250600-41258600	Weak transcription	Aorta	Aorta
31	chr15:41250800-41252400	Weak transcription	Placenta	Placenta
32	chr15:41250800-41252800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:41250800-41258000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:41250800-41258200	Weak transcription	HSMMtube	muscle
35	chr15:41251000-41253400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr15:41251200-41252400	Enhancers	H9 Cell Line	embryonic stem cell
37	chr15:41251200-41252600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:41251400-41253400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr15:41251800-41252400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41251800-41252400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr15:41251800-41252600	Enhancers	Primary B cells from peripheral blood	blood
42	chr15:41251800-41252800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:41251800-41252800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:41251800-41252800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:41251800-41252800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr15:41251800-41252800	Enhancers	Primary B cells from cord blood	blood
47	chr15:41251800-41252800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:41251800-41252800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:41251800-41252800	Enhancers	Fetal Thymus	thymus
50	chr15:41251800-41253000	Enhancers	Hela-S3	cervix

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