Variant report

Variant	rs11633799
Chromosome Location	chr15:41576538-41576539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41522897..41527944-chr15:41573906..41578128,9	K562	blood:
2	chr15:41573497..41577986-chr15:41624362..41627823,9	K562	blood:
3	chr15:41575391..41577503-chr15:41623750..41625308,2	MCF-7	breast:
4	chr15:41548966..41550602-chr15:41575421..41577159,2	MCF-7	breast:
5	chr15:41575813..41576546-chrX:77150464..77151239,2	Hela-S3	cervix:
6	chr15:41575902..41576619-chr2:217363468..217364442,2	Hela-S3	cervix:
7	chr14:51706560..51707399-chr15:41576064..41576687,2	Hela-S3	cervix:
8	chr15:41576500..41578232-chr15:41585051..41586799,2	K562	blood:
9	chr1:154154878..154155675-chr15:41576129..41576663,2	Hela-S3	cervix:
10	chr15:41407604..41409854-chr15:41574990..41577590,2	K562	blood:
11	chr15:41575115..41577125-chr15:41624466..41626801,3	MCF-7	breast:
12	chr15:41574856..41577423-chr15:41692996..41695992,2	K562	blood:
13	chr11:66035942..66036494-chr15:41576128..41576906,2	Hela-S3	cervix:
14	chr15:41575902..41576723-chr20:48789103..48789610,2	Hela-S3	cervix:
15	chr15:41576041..41576567-chr6:26198868..26199859,2	Hela-S3	cervix:
16	chr15:41522629..41527275-chr15:41575215..41577611,6	K562	blood:
17	chr15:41576033..41576699-chr17:5389238..5390221,2	Hela-S3	cervix:
18	chr15:41575029..41577348-chr15:41624329..41626974,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167842	Chromatin interaction
ENSG00000197756	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000178997	Chromatin interaction
ENSG00000174903	Chromatin interaction
ENSG00000072849	Chromatin interaction
ENSG00000102158	Chromatin interaction
ENSG00000231742	Chromatin interaction
ENSG00000137806	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000232485	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000139921	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000197846	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10152497	0.84[ASN][1000 genomes]
rs10152702	0.85[ASN][1000 genomes]
rs10153010	0.84[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10518718	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11549913	0.91[ASN][1000 genomes]
rs11630191	0.82[ASN][1000 genomes]
rs11631770	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs11852609	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857631	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324291	0.87[ASN][1000 genomes]
rs13379756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs16971767	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16971798	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs16971832	0.91[JPT][hapmap]
rs2015781	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2777491	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs28393472	0.84[ASN][1000 genomes]
rs28526381	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28557159	0.90[GIH][hapmap];0.84[MEX][hapmap]
rs28578057	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28583065	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28600680	0.88[ASN][1000 genomes]
rs28643296	0.91[ASN][1000 genomes]
rs28716108	0.90[ASN][1000 genomes]
rs28792672	0.86[ASN][1000 genomes]
rs316605	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs316609	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs316610	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs316614	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs35826725	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3743038	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs55782852	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58335029	0.87[ASN][1000 genomes]
rs58910172	0.91[ASN][1000 genomes]
rs59590312	0.86[ASN][1000 genomes]
rs61037359	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61127691	0.91[ASN][1000 genomes]
rs6650519	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66538814	0.88[ASN][1000 genomes]
rs7161772	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163649	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7163788	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs7165675	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7167729	0.83[ASN][1000 genomes]
rs7168177	0.82[ASN][1000 genomes]
rs7168307	0.90[GIH][hapmap];0.84[MEX][hapmap]
rs7175690	0.91[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176314	0.91[ASN][1000 genomes]
rs7176505	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176588	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177641	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs7178634	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs7178777	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs7180418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs7181560	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7181911	0.88[ASN][1000 genomes]
rs7182667	0.87[ASN][1000 genomes]
rs7183337	0.87[ASN][1000 genomes]
rs73404980	0.84[ASN][1000 genomes]
rs73404987	0.90[ASN][1000 genomes]
rs73404994	0.84[ASN][1000 genomes]
rs73404995	0.84[ASN][1000 genomes]
rs73404996	0.84[ASN][1000 genomes]
rs73405000	0.82[ASN][1000 genomes]
rs73405001	0.82[ASN][1000 genomes]
rs73407109	0.84[ASN][1000 genomes]
rs8023530	0.90[GIH][hapmap];0.84[MEX][hapmap]
rs8023619	0.90[ASN][1000 genomes]
rs8026197	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8027626	0.83[ASN][1000 genomes]
rs8032838	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034626	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036498	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037574	0.90[GIH][hapmap];0.84[MEX][hapmap]
rs8037824	0.82[ASN][1000 genomes]
rs8041325	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs823716	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs919961	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9302109	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9672866	0.81[ASN][1000 genomes]
rs9972288	0.86[ASN][1000 genomes]
rs9972547	0.88[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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs11633799	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11633799	NDUFAF1	cis	cerebellum	SCAN
rs11633799	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11633799	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11633799	NDUFAF1	cis	lymphoblastoid	seeQTL
rs11633799	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11633799	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11633799	RPAP1	cis	parietal	SCAN
rs11633799	CASC5	cis	cerebellum	SCAN
rs11633799	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs11633799	NDUFAF1	cis	parietal	SCAN
rs11633799	NDUFAF1	cis	Thyroid	GTEx
rs11633799	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11633799	NUSAP1	cis	parietal	SCAN
rs11633799	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11633799	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs11633799	NDUFAF1	cis	multi-tissue	Pritchard
rs11633799	OIP5-AS1	cis	Artery Tibial	GTEx
rs11633799	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11633799	NUSAP1	cis	cerebellum	SCAN
rs11633799	ZFP106	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41575200-41577200	Active TSS	Brain Substantia Nigra	brain
2	chr15:41575200-41577800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:41575400-41576800	Active TSS	Primary T cells from cord blood	blood
4	chr15:41575400-41577000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:41575400-41577000	Active TSS	Rectal Smooth Muscle	rectum
6	chr15:41575400-41577200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:41575400-41577200	Active TSS	Brain Anterior Caudate	brain
8	chr15:41575400-41577400	Active TSS	Brain Angular Gyrus	brain
9	chr15:41575400-41577400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:41575400-41577400	Active TSS	Fetal Stomach	stomach
11	chr15:41575400-41577400	Active TSS	HSMM	muscle
12	chr15:41575400-41577600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr15:41575400-41577600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:41575400-41577600	Active TSS	Brain Hippocampus Middle	brain
15	chr15:41575400-41577600	Active TSS	Psoas Muscle	Psoas
16	chr15:41575400-41577600	Active TSS	Stomach Smooth Muscle	stomach
17	chr15:41575400-41577800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:41575400-41577800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr15:41575400-41578400	Active TSS	Fetal Brain Female	brain
20	chr15:41575600-41576800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:41575600-41576800	Active TSS	Monocytes-CD14+_RO01746	blood
22	chr15:41575600-41577000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:41575600-41577000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:41575600-41577000	Active TSS	Osteobl	bone
25	chr15:41575600-41577200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr15:41575600-41577200	Active TSS	Thymus	Thymus
27	chr15:41575600-41577400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:41575600-41577400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr15:41575600-41577400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:41575600-41577400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:41575600-41577400	Active TSS	Brain Cingulate Gyrus	brain
32	chr15:41575600-41577400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr15:41575600-41577400	Active TSS	Colon Smooth Muscle	Colon
34	chr15:41575600-41577400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr15:41575600-41577400	Active TSS	Fetal Lung	lung
36	chr15:41575600-41577400	Active TSS	Left Ventricle	heart
37	chr15:41575600-41577400	Active TSS	Pancreas	Pancrea
38	chr15:41575600-41577400	Active TSS	Right Ventricle	heart
39	chr15:41575600-41577600	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr15:41575600-41577600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:41575600-41577600	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr15:41575600-41577800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr15:41575600-41577800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr15:41575600-41577800	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:41575600-41577800	Active TSS	Fetal Kidney	kidney
46	chr15:41575600-41577800	Active TSS	Ovary	ovary
47	chr15:41575600-41577800	Active TSS	GM12878-XiMat	blood
48	chr15:41575600-41578000	Active TSS	Brain Germinal Matrix	brain
49	chr15:41575600-41578000	Active TSS	Fetal Heart	heart
50	chr15:41575600-41578000	Active TSS	Right Atrium	heart

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