Variant report

Variant	rs11857631
Chromosome Location	chr15:41567369-41567370
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10152702	0.96[ASN][1000 genomes]
rs11549913	0.90[ASN][1000 genomes]
rs11633799	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852609	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971767	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16971798	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2015781	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28526381	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28578057	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28583065	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28600680	0.81[AMR][1000 genomes]
rs55782852	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59590312	0.83[AMR][1000 genomes]
rs61037359	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6650519	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7161772	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163649	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165675	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167498	0.81[ASN][1000 genomes]
rs7176505	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7176588	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181560	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181911	0.81[AMR][1000 genomes]
rs7182700	0.80[AMR][1000 genomes]
rs8023619	0.83[ASN][1000 genomes]
rs8032838	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8034626	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8036498	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs919961	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9302109	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9972547	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11857631	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11857631	NDUFAF1	cis	multi-tissue	Pritchard
rs11857631	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11857631	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11857631	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11857631	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11857631	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11857631	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs11857631	OIP5-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11857631	NDUFAF1	cis	Thyroid	GTEx
rs11857631	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11857631	OIP5-AS1	cis	Artery Tibial	GTEx
rs11857631	NDUFAF1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:41537400-41570800	Weak transcription	Ovary	ovary
6	chr15:41542800-41572000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:41545000-41571400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:41550400-41571400	Weak transcription	Right Ventricle	heart
11	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
12	chr15:41551800-41568600	Weak transcription	Fetal Lung	lung
13	chr15:41551800-41570600	Weak transcription	HMEC	breast
14	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
16	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:41553600-41569200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:41554600-41573000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:41555400-41569000	Weak transcription	Fetal Kidney	kidney
20	chr15:41555400-41570800	Weak transcription	HSMM	muscle
21	chr15:41555600-41569000	Weak transcription	Dnd41	blood
22	chr15:41555600-41570600	Strong transcription	Liver	Liver
23	chr15:41556200-41569000	Weak transcription	K562	blood
24	chr15:41556400-41571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:41556400-41574400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:41556600-41568400	Weak transcription	Stomach Mucosa	stomach
27	chr15:41556600-41568600	Weak transcription	NH-A	brain
28	chr15:41556600-41570800	Weak transcription	Brain Substantia Nigra	brain
29	chr15:41556800-41569200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:41556800-41569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:41556800-41571600	Weak transcription	Thymus	Thymus
32	chr15:41556800-41571800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:41556800-41572600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:41556800-41573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:41556800-41575200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:41556800-41575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:41556800-41575400	Weak transcription	Psoas Muscle	Psoas
38	chr15:41556800-41575800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:41556800-41575800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41557000-41568400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:41557000-41575400	Weak transcription	Fetal Heart	heart
42	chr15:41557200-41569000	Weak transcription	Fetal Brain Female	brain
43	chr15:41557200-41570800	Weak transcription	Brain Anterior Caudate	brain
44	chr15:41557200-41575200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:41557200-41575200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:41557400-41571600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:41557800-41572800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:41558200-41568800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:41559000-41571600	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:41559000-41575400	Weak transcription	Brain Germinal Matrix	brain

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