Variant report

Variant	rs11629979
Chromosome Location	chr15:41626579-41626580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPD	chr15:41626559-41627130	K562	blood:	n/a	n/a
2	RCOR1	chr15:41626577-41627070	K562	blood:	n/a	n/a
3	WRNIP1	chr15:41626572-41626983	GM12878	blood:	n/a	n/a
4	NR2F2	chr15:41626415-41627198	K562	blood:	n/a	n/a
5	TEAD4	chr15:41626554-41627259	K562	blood:	n/a	n/a
6	POLR2A	chr15:41626542-41627048	K562	blood:	n/a	n/a
7	GATA2	chr15:41626579-41627103	K562	blood:	n/a	chr15:41626884-41626895
8	GATA1	chr15:41626542-41627297	PBDE	blood:	n/a	chr15:41626884-41626895
9	POLR2A	chr15:41626561-41627147	GM12878	blood:	n/a	n/a
10	CCNT2	chr15:41626520-41627036	K562	blood:	n/a	n/a
11	GTF3C2	chr15:41625093-41627178	Hela-S3	cervix:	n/a	n/a
12	KAP1	chr15:41626194-41627237	HEK293	kidney:	n/a	n/a
13	RPC155	chr15:41625640-41626874	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr15:41626516-41627112	K562	blood:	n/a	n/a
15	PML	chr15:41626563-41627115	K562	blood:	n/a	n/a
16	HEY1	chr15:41626501-41626919	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41406745..41409392-chr15:41623521..41626579,5	K562	blood:
2	chr15:41625051..41627000-chr15:41692954..41695637,2	K562	blood:
3	chr15:41573497..41577986-chr15:41624362..41627823,9	K562	blood:
4	chr15:41575115..41577125-chr15:41624466..41626801,3	MCF-7	breast:
5	chr15:41314841..41316914-chr15:41624845..41626746,2	K562	blood:
6	chr15:41624254..41626833-chr15:41952098..41954867,2	K562	blood:
7	chr15:41575029..41577348-chr15:41624329..41626974,5	K562	blood:

No data

Variant related genes	Relation type
OIP5	TF binding region
ENSG00000137806	Chromatin interaction
ENSG00000259521	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000174197	Chromatin interaction
ENSG00000247556	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10518717	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132639	0.83[EUR][1000 genomes]
rs11630656	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	1.00[ASN][1000 genomes]
rs13313520	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	1.00[ASN][1000 genomes]
rs17730589	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	1.00[ASN][1000 genomes]
rs2118740	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28377562	0.94[AMR][1000 genomes];0.95[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	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.87[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28463309	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.81[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[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.85[EUR][1000 genomes]
rs56400990	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.89[AMR][1000 genomes];0.95[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	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	1.00[ASN][1000 genomes]
rs7164684	1.00[ASN][1000 genomes]
rs7165396	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[ASN][1000 genomes]
rs7169543	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.85[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11629979	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11629979	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11629979	OIP5-AS1	cis	Artery Tibial	GTEx
rs11629979	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11629979	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11629979	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11629979	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11629979	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs11629979	NDUFAF1	cis	Thyroid	GTEx
rs11629979	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11629979	NDUFAF1	cis	multi-tissue	Pritchard
rs11629979	LOC729082	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41623000-41626800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41623000-41627200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:41623000-41627200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:41623000-41627200	Active TSS	A549	lung
5	chr15:41623000-41627400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41623400-41627000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41623400-41627200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:41623400-41627200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr15:41623400-41627400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:41623600-41626800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41623600-41626800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:41623600-41626800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41623600-41627000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:41623600-41627000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr15:41623600-41627200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:41623600-41627200	Active TSS	Thymus	Thymus
17	chr15:41623600-41627200	Active TSS	Hela-S3	cervix
18	chr15:41623800-41626600	Active TSS	Fetal Thymus	thymus
19	chr15:41623800-41626800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:41623800-41627200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:41623800-41627200	Active TSS	NHDF-Ad	bronchial
22	chr15:41623800-41627400	Active TSS	GM12878-XiMat	blood
23	chr15:41623800-41627400	Active TSS	K562	blood
24	chr15:41624000-41626600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:41624000-41626600	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr15:41624000-41626600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:41624000-41626600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:41624000-41626600	Active TSS	NHEK	skin
29	chr15:41624000-41626800	Active TSS	Fetal Intestine Small	intestine
30	chr15:41624000-41627200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr15:41624000-41627400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr15:41624200-41626600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:41624200-41626600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr15:41624200-41626800	Active TSS	Fetal Kidney	kidney
35	chr15:41624200-41626800	Active TSS	NHLF	lung
36	chr15:41624200-41627000	Active TSS	Fetal Lung	lung
37	chr15:41624200-41627200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:41624200-41627200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:41624200-41627200	Active TSS	HSMM	muscle
40	chr15:41624200-41627400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr15:41624400-41626600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:41624400-41626800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:41624400-41626800	Active TSS	Rectal Smooth Muscle	rectum
44	chr15:41624400-41627000	Active TSS	Fetal Brain Female	brain
45	chr15:41624400-41627000	Active TSS	NH-A	brain
46	chr15:41624800-41626600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:41624800-41626600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:41625200-41627000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:41625400-41626800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:41625400-41670200	Weak transcription	Gastric	stomach

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