Variant report

Variant	rs9302109
Chromosome Location	chr15:41612180-41612181
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41601722..41603239-chr15:41610507..41613182,2	K562	blood:
2	chr15:41601722..41604409-chr15:41611682..41614263,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10152497	0.89[ASN][1000 genomes]
rs10153010	0.89[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10518718	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11549913	0.85[ASN][1000 genomes]
rs11630191	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
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];0.86[ASN][1000 genomes]
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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852609	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857631	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12324291	0.92[ASN][1000 genomes]
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];0.81[LWK][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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
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];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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];0.86[ASN][1000 genomes]
rs28393472	0.89[ASN][1000 genomes]
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];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs28578057	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583065	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600680	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28643296	0.96[ASN][1000 genomes]
rs28655070	0.82[ASN][1000 genomes]
rs28716108	0.95[ASN][1000 genomes]
rs28792672	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[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];0.86[ASN][1000 genomes]
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]
rs316613	0.83[ASN][1000 genomes]
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];0.83[ASN][1000 genomes]
rs316615	0.80[ASN][1000 genomes]
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];0.83[ASN][1000 genomes]
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];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55782852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58335029	0.92[ASN][1000 genomes]
rs58910172	0.96[ASN][1000 genomes]
rs59590312	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61037359	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61127691	0.96[ASN][1000 genomes]
rs6650519	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66538814	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161772	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163649	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165675	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7167729	0.88[ASN][1000 genomes]
rs7168177	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7168307	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs7172148	0.83[ASN][1000 genomes]
rs7175690	0.96[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7176314	0.96[ASN][1000 genomes]
rs7176505	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.86[ASN][1000 genomes]
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];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7178777	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]
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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7181560	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181911	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182667	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7182700	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7183337	0.92[ASN][1000 genomes]
rs73404980	0.89[ASN][1000 genomes]
rs73404987	0.95[ASN][1000 genomes]
rs73404994	0.89[ASN][1000 genomes]
rs73404995	0.89[ASN][1000 genomes]
rs73404996	0.89[ASN][1000 genomes]
rs73405000	0.87[ASN][1000 genomes]
rs73405001	0.87[ASN][1000 genomes]
rs73407109	0.89[ASN][1000 genomes]
rs8023530	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs8023619	0.92[ASN][1000 genomes]
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];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027626	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034626	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034819	0.83[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs8037824	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
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];0.81[ASN][1000 genomes]
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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672866	0.85[ASN][1000 genomes]
rs9972288	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9972547	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	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
4	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
5	esv14767	chr15:41595813-41619355	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv977843	chr15:41608625-41625613	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs9302109	OIP5-AS1	cis	Nerve Tibial	GTEx
rs9302109	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs9302109	NUSAP1	cis	cerebellum	SCAN
rs9302109	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs9302109	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs9302109	NDUFAF1	cis	cerebellum	SCAN
rs9302109	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs9302109	RPAP1	cis	parietal	SCAN
rs9302109	OIP5-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs9302109	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs9302109	NDUFAF1	cis	Muscle Skeletal	GTEx
rs9302109	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs9302109	NDUFAF1	cis	parietal	SCAN
rs9302109	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs9302109	NDUFAF1	cis	multi-tissue	Pritchard
rs9302109	NUSAP1	cis	parietal	SCAN
rs9302109	NDUFAF1	cis	lymphoblastoid	seeQTL
rs9302109	CASC5	cis	cerebellum	SCAN
rs9302109	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs9302109	OIP5-AS1	cis	Artery Tibial	GTEx
rs9302109	NDUFAF1	cis	Thyroid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
3	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
4	chr15:41583200-41623600	Weak transcription	HSMM	muscle
5	chr15:41583800-41613000	Weak transcription	Right Ventricle	heart
6	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
7	chr15:41587600-41623000	Weak transcription	NHEK	skin
8	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
9	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:41590600-41623000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:41590800-41623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle
14	chr15:41591600-41623200	Weak transcription	HUVEC	blood vessel
15	chr15:41591800-41624000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:41592000-41618400	Weak transcription	Fetal Brain Female	brain
17	chr15:41592400-41623000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:41592400-41623200	Weak transcription	Osteobl	bone
19	chr15:41592400-41624000	Weak transcription	Brain Angular Gyrus	brain
20	chr15:41592600-41612400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:41592600-41623800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:41592800-41612400	Weak transcription	Fetal Intestine Large	intestine
23	chr15:41592800-41613200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:41593600-41623800	Weak transcription	NH-A	brain
25	chr15:41597200-41623000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:41597200-41623000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:41599800-41612200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:41600600-41623600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:41602400-41623000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:41602400-41623600	Weak transcription	NHDF-Ad	bronchial
31	chr15:41603200-41613200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:41603400-41614000	Weak transcription	Primary T cells from cord blood	blood
33	chr15:41603400-41618600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:41603400-41622800	Weak transcription	HepG2	liver
35	chr15:41603400-41623000	Weak transcription	Brain Germinal Matrix	brain
36	chr15:41603400-41623400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:41603600-41612200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:41603600-41618600	Weak transcription	A549	lung
39	chr15:41603800-41615000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:41603800-41623600	Weak transcription	Fetal Lung	lung
41	chr15:41604000-41623200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:41604200-41624000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:41604800-41612400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:41605400-41623200	Weak transcription	HMEC	breast
45	chr15:41605600-41612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:41605800-41615400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:41605800-41623400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:41605800-41623800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:41605800-41623800	Weak transcription	Adipose Nuclei	Adipose
50	chr15:41606200-41623000	Weak transcription	Hela-S3	cervix

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