Variant report

Variant	rs11630656
Chromosome Location	chr15:41570909-41570910
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10518717	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs11854820	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs13313520	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs1757468	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17730589	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs2118740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap];0.80[MEX][hapmap]
rs28377562	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28437576	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	1.00[AFR][1000 genomes]
rs28463309	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs316604	1.00[ASN][1000 genomes]
rs316606	1.00[ASN][1000 genomes]
rs316607	1.00[ASN][1000 genomes]
rs316611	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34040639	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[TSI][hapmap]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55725658	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.89[EUR][1000 genomes]
rs56400990	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7164684	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.85[EUR][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs11630656	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11630656	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11630656	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11630656	SPINT1	cis	cerebellum	SCAN
rs11630656	NDUFAF1	cis	parietal	SCAN
rs11630656	NDUFAF1	cis	Thyroid	GTEx
rs11630656	GPR176	cis	parietal	SCAN
rs11630656	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11630656	KRTAP4-7	cis	lesional skin	skin_eQTL
rs11630656	CASC5	cis	cerebellum	SCAN
rs11630656	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11630656	NUSAP1	cis	parietal	SCAN
rs11630656	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11630656	NDUFAF1	cis	lymphoblastoid	seeQTL
rs11630656	KRTAP4-7	cis	normal skin	skin_eQTL
rs11630656	RASGRP1	cis	cerebellum	SCAN
rs11630656	OIP5-AS1	cis	Artery Tibial	GTEx
rs11630656	NUSAP1	cis	cerebellum	SCAN
rs11630656	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11630656	NDUFAF1	cis	cerebellum	SCAN
rs11630656	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11630656	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs11630656	NDUFAF1	cis	lung	GTEx
rs11630656	ITPKA	cis	lymphoblastoid	seeQTL
rs11630656	NDUFAF1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr15:41542800-41572000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:41545000-41571400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:41550400-41571400	Weak transcription	Right Ventricle	heart
10	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
11	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
13	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:41554600-41573000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:41556400-41571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:41556400-41574400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:41556800-41571600	Weak transcription	Thymus	Thymus
18	chr15:41556800-41571800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:41556800-41572600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:41556800-41573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:41556800-41575200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:41556800-41575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:41556800-41575400	Weak transcription	Psoas Muscle	Psoas
24	chr15:41556800-41575800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:41556800-41575800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:41557000-41575400	Weak transcription	Fetal Heart	heart
27	chr15:41557200-41575200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:41557200-41575200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:41557400-41571600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:41557800-41572800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:41559000-41571600	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:41559000-41575400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:41561200-41572600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:41561600-41572600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:41561600-41572800	Strong transcription	Adipose Nuclei	Adipose
36	chr15:41561800-41572600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:41562000-41572600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:41562000-41572600	Strong transcription	Fetal Stomach	stomach
39	chr15:41562000-41573200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:41562000-41574000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:41562400-41572600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:41562800-41572600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:41563000-41571600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:41563000-41575400	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:41564000-41575400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:41564000-41575400	Weak transcription	HUVEC	blood vessel
47	chr15:41564200-41571000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:41564200-41575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:41564200-41575400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:41564200-41576200	Weak transcription	Small Intestine	intestine

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