Variant report

Variant	rs11630191
Chromosome Location	chr15:41701021-41701022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41696803..41699662-chr15:41700695..41704414,5	MCF-7	breast:
2	chr15:41696720..41701906-chr15:41705029..41710558,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10152497	0.89[ASN][1000 genomes]
rs10153010	0.89[ASN][1000 genomes]
rs10467974	0.81[ASN][1000 genomes]
rs10518718	0.84[ASN][1000 genomes]
rs11631770	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633799	0.82[ASN][1000 genomes]
rs11852609	0.81[EUR][1000 genomes]
rs12324291	0.87[ASN][1000 genomes]
rs1655556	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16971767	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16971798	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16971806	0.95[ASN][1000 genomes]
rs16971832	0.83[ASN][1000 genomes]
rs16971834	0.82[ASN][1000 genomes]
rs1757455	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015781	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2777491	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28393472	0.89[ASN][1000 genomes]
rs28526381	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28578057	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28583065	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28600680	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28643296	0.83[ASN][1000 genomes]
rs28655070	0.92[ASN][1000 genomes]
rs28716108	0.89[ASN][1000 genomes]
rs28792672	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28847691	0.89[ASN][1000 genomes]
rs316605	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316609	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316610	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316613	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316614	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316615	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35826725	0.93[ASN][1000 genomes]
rs3743038	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55782852	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58910172	0.83[ASN][1000 genomes]
rs59590312	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61037359	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61127691	0.83[ASN][1000 genomes]
rs6650519	0.84[ASN][1000 genomes]
rs66538814	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66591771	0.82[EUR][1000 genomes]
rs7161772	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163649	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7163788	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165675	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167498	0.82[ASN][1000 genomes]
rs7167729	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7168177	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172148	0.93[ASN][1000 genomes]
rs7175690	0.83[ASN][1000 genomes]
rs7175800	0.83[ASN][1000 genomes]
rs7176314	0.83[ASN][1000 genomes]
rs7176505	0.81[EUR][1000 genomes]
rs7176588	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7177641	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7180492	0.84[ASN][1000 genomes]
rs7181560	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7181911	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182667	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182700	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73404987	0.84[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]
rs8026197	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027626	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032838	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034626	0.85[ASN][1000 genomes]
rs8034819	0.93[ASN][1000 genomes]
rs8036498	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036527	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8037824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs823716	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs919961	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9302109	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9672866	0.85[ASN][1000 genomes]
rs9972288	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv569232	chr15:41694377-41730246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11630191	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11630191	OIP5-AS1	cis	Artery Tibial	GTEx
rs11630191	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs11630191	NDUFAF1	cis	Thyroid	GTEx
rs11630191	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs11630191	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11630191	OIP5-AS1	cis	Nerve Tibial	GTEx
rs11630191	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs11630191	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs11630191	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41695400-41703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:41695400-41707800	Weak transcription	HSMMtube	muscle
3	chr15:41695400-41708400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:41695600-41701800	Weak transcription	K562	blood
5	chr15:41695600-41707600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:41695600-41707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:41695600-41708400	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:41696000-41701600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:41696000-41701800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:41697400-41707800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:41699200-41703400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:41699600-41701600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr15:41699600-41706400	Weak transcription	HepG2	liver
14	chr15:41700000-41702000	Enhancers	Primary B cells from cord blood	blood
15	chr15:41700200-41701200	Enhancers	Placenta	Placenta
16	chr15:41700200-41702000	Weak transcription	A549	lung
17	chr15:41700600-41701600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr15:41700600-41707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:41700600-41707800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:41700800-41701800	Weak transcription	Fetal Intestine Large	intestine
21	chr15:41700800-41702000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:41700800-41702000	Weak transcription	Fetal Intestine Small	intestine
23	chr15:41700800-41703000	Weak transcription	Stomach Mucosa	stomach
24	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:41700800-41703400	Weak transcription	NHEK	skin
27	chr15:41700800-41707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:41700800-41707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:41701000-41701400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:41701000-41708000	Weak transcription	Lung	lung

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