Variant report

Variant	rs28538500
Chromosome Location	chr15:41256265-41256266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41220857..41223569-chr15:41256208..41258931,3	MCF-7	breast:
2	chr15:41232446..41235218-chr15:41255104..41257063,2	K562	blood:

Variant related genes	Relation type
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1001341	0.87[EUR][1000 genomes]
rs11070313	0.88[AFR][1000 genomes]
rs11070314	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070315	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070317	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070318	0.88[ASN][1000 genomes]
rs11854054	0.92[AFR][1000 genomes]
rs11855248	0.83[EUR][1000 genomes]
rs12593739	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12899590	0.84[EUR][1000 genomes]
rs12905926	0.80[EUR][1000 genomes]
rs12910027	0.80[EUR][1000 genomes]
rs12912887	0.88[ASN][1000 genomes]
rs1869907	0.91[EUR][1000 genomes]
rs1869908	0.88[ASN][1000 genomes]
rs2305656	0.81[ASN][1000 genomes]
rs2412572	0.85[EUR][1000 genomes]
rs2412574	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28479904	0.84[EUR][1000 genomes]
rs28501589	0.82[EUR][1000 genomes]
rs28572344	0.81[EUR][1000 genomes]
rs2899002	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][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	0.89[EUR][1000 genomes]
rs4924520	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924521	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924522	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924523	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4924524	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4924525	0.92[EUR][1000 genomes]
rs4924526	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924528	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60588038	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162992	0.80[EUR][1000 genomes]
rs7169669	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7174555	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72735675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030306	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8042127	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8042230	0.86[AFR][1000 genomes]
rs9796	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9920619	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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
rs28538500	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41246400-41268200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41246600-41258200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:41246600-41270000	Weak transcription	HUVEC	blood vessel
4	chr15:41246800-41268000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:41246800-41268200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41249000-41258400	Weak transcription	K562	blood
7	chr15:41249400-41266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:41249400-41268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:41249600-41258600	Weak transcription	NHLF	lung
10	chr15:41250000-41258400	Weak transcription	Right Atrium	heart
11	chr15:41250000-41264400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:41250600-41258200	Weak transcription	Left Ventricle	heart
13	chr15:41250600-41258600	Weak transcription	Aorta	Aorta
14	chr15:41250800-41258000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:41250800-41258200	Weak transcription	HSMMtube	muscle
16	chr15:41252400-41269400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:41252600-41258400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:41252800-41258200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:41252800-41258400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:41252800-41261000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:41252800-41270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:41253000-41258200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:41253400-41257400	Weak transcription	Fetal Intestine Small	intestine
24	chr15:41253400-41258400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:41253600-41258400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:41253600-41268200	Weak transcription	Spleen	Spleen
27	chr15:41253600-41268800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:41253600-41268800	Weak transcription	Right Ventricle	heart
29	chr15:41253800-41257600	Weak transcription	Stomach Mucosa	stomach
30	chr15:41255800-41260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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