Variant report

Variant	rs7178777
Chromosome Location	chr15:41634588-41634589
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41633465-41634732	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41623748..41626097-chr15:41632335..41635242,3	K562	blood:

Variant related genes	Relation type
NUSAP1	TF binding region
ENSG00000259396	TF binding region
ENSG00000137804	Chromatin interaction
ENSG00000104147	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10467974	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10518718	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs11631770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs11633799	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]
rs13379756	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs16971767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs16971798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs16971806	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs16971832	0.91[JPT][hapmap]
rs16971834	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs1757456	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs1757463	0.87[CHB][hapmap]
rs2015781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs2777491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs28526381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs28557159	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs28578057	0.82[ASN][1000 genomes]
rs28583065	0.82[ASN][1000 genomes]
rs316605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs316609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs316610	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs316614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs316617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs35826725	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3743038	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs55782852	0.82[ASN][1000 genomes]
rs58335029	0.80[ASN][1000 genomes]
rs61037359	0.80[ASN][1000 genomes]
rs7161772	0.82[ASN][1000 genomes]
rs7163649	0.80[ASN][1000 genomes]
rs7163788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7165675	0.82[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7168307	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs7175800	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7176588	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs7177641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7178634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7180418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7181560	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7183337	0.80[ASN][1000 genomes]
rs73404980	0.80[ASN][1000 genomes]
rs8023530	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs8024774	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[TSI][hapmap]
rs8026197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8032838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs8036498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs8037574	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs8041325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs823716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs919961	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs9302109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7178777	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs7178777	RPAP1	cis	parietal	SCAN
rs7178777	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7178777	NUSAP1	cis	cerebellum	SCAN
rs7178777	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7178777	OIP5-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7178777	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7178777	NDUFAF1	cis	Thyroid	GTEx
rs7178777	NUSAP1	cis	parietal	SCAN
rs7178777	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7178777	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7178777	CASC5	cis	cerebellum	SCAN
rs7178777	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs7178777	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7178777	OIP5-AS1	cis	Artery Tibial	GTEx
rs7178777	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7178777	NDUFAF1	cis	cerebellum	SCAN
rs7178777	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7178777	NDUFAF1	cis	parietal	SCAN
rs7178777	NDUFAF1	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625400-41670200	Weak transcription	Gastric	stomach
2	chr15:41625600-41659200	Weak transcription	Lung	lung
3	chr15:41625800-41665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
5	chr15:41626000-41642000	Weak transcription	Ovary	ovary
6	chr15:41626000-41665200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:41626200-41640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:41626200-41643400	Weak transcription	Spleen	Spleen
9	chr15:41626200-41658200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:41626200-41678200	Weak transcription	Liver	Liver
11	chr15:41626200-41680200	Weak transcription	Fetal Brain Male	brain
12	chr15:41626400-41677800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:41626400-41678400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:41626600-41643400	Weak transcription	Primary B cells from cord blood	blood
15	chr15:41626800-41641200	Weak transcription	Placenta	Placenta
16	chr15:41626800-41642800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:41626800-41643200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:41626800-41643400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:41627000-41638000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:41627000-41672800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:41627200-41637000	Weak transcription	Brain Germinal Matrix	brain
23	chr15:41627200-41676800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:41627400-41668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:41627400-41673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:41628200-41673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:41628600-41672800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:41628600-41673800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:41628800-41654400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:41629000-41672000	Weak transcription	Primary T cells from cord blood	blood
31	chr15:41629000-41673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:41629400-41672400	Strong transcription	Fetal Stomach	stomach
33	chr15:41629400-41672800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:41629400-41673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:41629600-41674000	Strong transcription	Fetal Thymus	thymus
36	chr15:41629800-41658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:41630000-41662000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:41630400-41649600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:41630400-41674000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:41630400-41674200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr15:41630600-41635600	Strong transcription	HUVEC	blood vessel
42	chr15:41630800-41636800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:41630800-41642800	Weak transcription	Fetal Heart	heart
44	chr15:41630800-41673800	Strong transcription	Dnd41	blood
45	chr15:41631200-41643400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:41631200-41659200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr15:41631800-41649600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:41631800-41679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:41632000-41654600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:41632000-41673000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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