Variant report

Variant	rs8042088
Chromosome Location	chr15:41337487-41337488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41330998..41333072-chr15:41336486..41338381,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070315	1.00[CEU][hapmap]
rs11853192	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11854472	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11855248	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856572	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856577	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856848	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858678	0.82[MEX][hapmap]
rs12899590	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905926	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910027	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13329511	0.84[ASN][1000 genomes]
rs1678750	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1717200	0.91[EUR][1000 genomes]
rs1869907	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs1962410	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1983400	0.85[ASN][1000 genomes]
rs2176998	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306083	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412572	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412574	0.81[ASN][1000 genomes]
rs2412601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28455998	0.85[EUR][1000 genomes]
rs28473405	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28479904	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28501589	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28510775	0.85[ASN][1000 genomes]
rs28581803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28613002	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28688742	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28729675	0.86[EUR][1000 genomes]
rs28866311	0.85[EUR][1000 genomes]
rs2899002	1.00[CEU][hapmap]
rs2925342	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2925343	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2925346	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2927061	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2927062	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2928148	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2947493	0.86[ASN][1000 genomes]
rs2947494	0.86[ASN][1000 genomes]
rs3100807	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3101436	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3101442	0.85[EUR][1000 genomes]
rs3214068	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3986311	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4244584	0.82[ASN][1000 genomes]
rs4497658	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4592624	0.83[ASN][1000 genomes]
rs476633	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4923890	0.81[ASN][1000 genomes]
rs516156	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs544744	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57393155	0.87[EUR][1000 genomes]
rs66818965	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs690733	0.82[MEX][hapmap]
rs691830	0.90[EUR][1000 genomes]
rs692153	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs692155	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[EUR][1000 genomes]
rs7162992	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169375	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171437	0.84[ASN][1000 genomes]
rs7179681	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181816	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72737704	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023345	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030306	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8037837	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9796	0.96[CEU][hapmap]

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	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8042088	NDUFAF1	cis	lymphoblastoid	seeQTL
rs8042088	C15orf62	cis	parietal	SCAN
rs8042088	CASC5	cis	cerebellum	SCAN
rs8042088	NDUFAF1	cis	Muscle Skeletal	GTEx
rs8042088	BUB1B	cis	parietal	SCAN
rs8042088	NDUFAF1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:41306800-41338800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:41309000-41339200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:41319400-41339800	Weak transcription	Psoas Muscle	Psoas
7	chr15:41320600-41339400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:41324400-41350400	Weak transcription	Pancreas	Pancrea
9	chr15:41325600-41354000	Strong transcription	Primary B cells from peripheral blood	blood
10	chr15:41325800-41354000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:41327600-41339200	Weak transcription	Stomach Mucosa	stomach
12	chr15:41327800-41350800	Weak transcription	Aorta	Aorta
13	chr15:41328400-41353200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:41329400-41353000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:41329800-41353400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:41330000-41351600	Strong transcription	Primary T cells from cord blood	blood
18	chr15:41330200-41353400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:41330200-41354000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:41330400-41344000	Strong transcription	Hela-S3	cervix
21	chr15:41330400-41352400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:41330400-41352800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:41330400-41353000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41330400-41353000	Strong transcription	Dnd41	blood
25	chr15:41330400-41354000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:41330400-41354400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:41330600-41352800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:41330600-41353200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:41330600-41353600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:41330800-41339800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:41330800-41345400	Strong transcription	Fetal Lung	lung
32	chr15:41330800-41352200	Strong transcription	Primary B cells from cord blood	blood
33	chr15:41330800-41353000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:41330800-41353200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:41330800-41353200	Strong transcription	Fetal Thymus	thymus
36	chr15:41330800-41353400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:41330800-41353600	Strong transcription	Placenta	Placenta
38	chr15:41330800-41354600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:41331000-41339600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:41331000-41345400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:41331000-41352600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:41331000-41352800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:41331000-41355600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:41331200-41339600	Strong transcription	Fetal Intestine Large	intestine
45	chr15:41331200-41354000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr15:41331200-41354000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:41331400-41352200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:41331600-41352400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:41331600-41352800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:41332400-41355800	Strong transcription	Stomach Smooth Muscle	stomach

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