Variant report

Variant	rs11856169
Chromosome Location	chr15:41547938-41547939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10851403	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855906	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13329235	0.83[EUR][1000 genomes]
rs13329579	0.82[EUR][1000 genomes]
rs16971726	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374715	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28493087	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28524914	0.88[EUR][1000 genomes]
rs28554139	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671712	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28827035	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs513280	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs521890	0.81[EUR][1000 genomes]
rs522063	0.81[EUR][1000 genomes]
rs533210	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs691011	0.81[EUR][1000 genomes]
rs691629	0.81[EUR][1000 genomes]
rs691906	0.81[EUR][1000 genomes]
rs691907	0.81[EUR][1000 genomes]
rs72737786	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72737792	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72737793	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72739609	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8043237	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][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	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11856169	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11856169	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11856169	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11856169	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11856169	OIP5-AS1	cis	Artery Tibial	GTEx
rs11856169	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11856169	NDUFAF1	cis	multi-tissue	Pritchard
rs11856169	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11856169	NDUFAF1	cis	Thyroid	GTEx
rs11856169	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11856169	NDUFAF1	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41554800	Weak transcription	Fetal Thymus	thymus
2	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
3	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
4	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
7	chr15:41525000-41548400	Weak transcription	Fetal Lung	lung
8	chr15:41525200-41548200	Weak transcription	Fetal Kidney	kidney
9	chr15:41525200-41554200	Weak transcription	Fetal Brain Female	brain
10	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:41525400-41556200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:41525400-41556800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:41525800-41554800	Weak transcription	Dnd41	blood
15	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:41526000-41554800	Weak transcription	Brain Angular Gyrus	brain
17	chr15:41526200-41554800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:41532400-41550600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:41533200-41548400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:41533200-41552400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:41533800-41554600	Weak transcription	Brain Anterior Caudate	brain
22	chr15:41533800-41555000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:41534000-41555200	Weak transcription	Brain Germinal Matrix	brain
24	chr15:41534200-41551000	Weak transcription	GM12878-XiMat	blood
25	chr15:41534200-41555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:41534200-41556400	Weak transcription	Spleen	Spleen
27	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:41536800-41555000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:41536800-41555200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:41537000-41549800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:41537200-41548600	Weak transcription	HUVEC	blood vessel
32	chr15:41537200-41553000	Weak transcription	Colonic Mucosa	Colon
33	chr15:41537200-41555000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:41537400-41555000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:41537400-41570800	Weak transcription	Ovary	ovary
36	chr15:41537600-41552000	Weak transcription	Pancreas	Pancrea
37	chr15:41537600-41562800	Weak transcription	Lung	lung
38	chr15:41537800-41548600	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:41537800-41549800	Weak transcription	Right Ventricle	heart
40	chr15:41537800-41552000	Weak transcription	Psoas Muscle	Psoas
41	chr15:41537800-41554600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:41538000-41549200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:41538000-41550000	Weak transcription	Brain Substantia Nigra	brain
44	chr15:41538200-41555000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:41538600-41550000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:41538800-41549000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:41539400-41555000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:41539400-41555800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:41541600-41548800	Weak transcription	Placenta	Placenta
50	chr15:41541600-41549800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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