Variant report

Variant	rs11635906
Chromosome Location	chr15:41779260-41779261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
2	chr15:41777763..41779575-chr15:41786284..41787961,2	MCF-7	breast:
3	chr15:41777253..41780203-chr15:41850412..41852434,2	K562	blood:
4	chr15:41768675..41771107-chr15:41779166..41782529,4	K562	blood:

Variant related genes	Relation type
ENSG00000137815	Chromatin interaction
ENSG00000137825	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10518717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11070328	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11630799	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11854081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs11854632	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs13380007	0.88[YRI][hapmap]
rs1617832	0.93[YRI][hapmap]
rs1757468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs17730888	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	1.00[ASN][1000 genomes]
rs2730056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28416360	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28456082	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28459164	0.86[EUR][1000 genomes]
rs28463309	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs28477406	1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28555198	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28576457	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	1.00[ASN][1000 genomes]
rs28631111	1.00[CHB][hapmap]
rs28661013	1.00[ASN][1000 genomes]
rs28663426	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28897479	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316618	0.93[YRI][hapmap]
rs3204853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34285452	0.84[EUR][1000 genomes]
rs34665396	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924549	1.00[CHB][hapmap]
rs55725658	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400990	1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7168431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7181982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs72739644	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8034840	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs8036734	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8041809	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs11635906	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11635906	NDUFAF1	cis	Thyroid	GTEx
rs11635906	ZFP106	cis	parietal	SCAN
rs11635906	NUSAP1	cis	cerebellum	SCAN
rs11635906	OIP5-AS1	cis	Artery Tibial	GTEx
rs11635906	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs11635906	GPR176	cis	cerebellum	SCAN
rs11635906	RPAP1	cis	parietal	SCAN
rs11635906	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11635906	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11635906	NDUFAF1	cis	multi-tissue	Pritchard
rs11635906	NDUFAF1	cis	cerebellum	SCAN
rs11635906	GPR176	cis	parietal	SCAN
rs11635906	SPINT1	cis	cerebellum	SCAN
rs11635906	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11635906	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11635906	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11635906	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11635906	NDUFAF1	cis	lung	GTEx
rs11635906	NDUFAF1	cis	lymphoblastoid	seeQTL
rs11635906	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11635906	NUSAP1	cis	parietal	SCAN
rs11635906	NDUFAF1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41769600-41780200	Weak transcription	Right Atrium	heart
2	chr15:41771600-41780200	Weak transcription	Fetal Heart	heart
3	chr15:41773000-41779600	Weak transcription	HUVEC	blood vessel
4	chr15:41773400-41779600	Weak transcription	Colonic Mucosa	Colon
5	chr15:41773400-41785000	Weak transcription	A549	lung
6	chr15:41773800-41780000	Weak transcription	HMEC	breast
7	chr15:41773800-41780200	Weak transcription	NHLF	lung
8	chr15:41773800-41784000	Weak transcription	HepG2	liver
9	chr15:41774000-41779400	Weak transcription	Lung	lung
10	chr15:41774000-41782200	Weak transcription	Osteobl	bone
11	chr15:41774600-41779600	Weak transcription	NH-A	brain
12	chr15:41774800-41784600	Weak transcription	Dnd41	blood
13	chr15:41775000-41779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:41775000-41780400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:41775400-41779600	Weak transcription	Fetal Kidney	kidney
16	chr15:41775400-41780000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:41775400-41780000	Weak transcription	Esophagus	oesophagus
18	chr15:41775400-41780000	Weak transcription	Fetal Thymus	thymus
19	chr15:41775400-41780400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:41775400-41784800	Weak transcription	Liver	Liver
21	chr15:41775600-41780000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:41775600-41781800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:41775600-41781800	Weak transcription	NHDF-Ad	bronchial
24	chr15:41775600-41782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:41775600-41783800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:41775600-41784800	Weak transcription	Brain Angular Gyrus	brain
27	chr15:41775800-41780200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:41775800-41782200	Weak transcription	HSMMtube	muscle
29	chr15:41776000-41779400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:41776000-41779600	Weak transcription	Gastric	stomach
31	chr15:41776000-41779800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:41776000-41780000	Weak transcription	Fetal Lung	lung
33	chr15:41776000-41780000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:41776000-41780000	Weak transcription	HSMM	muscle
35	chr15:41776000-41781000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:41776000-41782000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:41776000-41782200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:41776000-41782400	Weak transcription	NHEK	skin
39	chr15:41776000-41782800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:41776000-41784400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:41776000-41784800	Weak transcription	Brain Germinal Matrix	brain
42	chr15:41776200-41779400	Weak transcription	Fetal Intestine Large	intestine
43	chr15:41776200-41782800	Weak transcription	Primary B cells from cord blood	blood
44	chr15:41776400-41779800	Weak transcription	GM12878-XiMat	blood
45	chr15:41776400-41780000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:41776400-41780000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:41776400-41783600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:41776400-41783800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:41776600-41779400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:41776800-41779400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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