Variant report

Variant	rs28555198
Chromosome Location	chr15:41701647-41701648
allele	A/C
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: 101 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10518717	1.00[ASN][1000 genomes]
rs11070328	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11630799	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs1757468	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	1.00[ASN][1000 genomes]
rs17730888	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	1.00[ASN][1000 genomes]
rs2730056	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28456082	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28463309	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	1.00[ASN][1000 genomes]
rs28576457	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34285452	0.88[EUR][1000 genomes]
rs34665396	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs55725658	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400990	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	1.00[ASN][1000 genomes]
rs7168431	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	1.00[ASN][1000 genomes]
rs7181982	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs72739644	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[ASN][1000 genomes]
rs8034840	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8041809	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	1.00[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28555198	NDUFAF1	cis	Thyroid	GTEx
rs28555198	NDUFAF1	cis	lung	GTEx
rs28555198	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28555198	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28555198	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28555198	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28555198	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28555198	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28555198	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28555198	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28555198	OIP5-AS1	cis	Artery Tibial	GTEx
rs28555198	NDUFAF1	cis	Whole Blood	GTEx
rs28555198	OIP5-AS1	cis	Nerve Tibial	GTEx

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	chr15:41696000-41701800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:41697400-41707800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:41699200-41703400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:41699600-41706400	Weak transcription	HepG2	liver
12	chr15:41700000-41702000	Enhancers	Primary B cells from cord blood	blood
13	chr15:41700200-41702000	Weak transcription	A549	lung
14	chr15:41700600-41707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:41700600-41707800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:41700800-41701800	Weak transcription	Fetal Intestine Large	intestine
17	chr15:41700800-41702000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:41700800-41702000	Weak transcription	Fetal Intestine Small	intestine
19	chr15:41700800-41703000	Weak transcription	Stomach Mucosa	stomach
20	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:41700800-41703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:41700800-41703400	Weak transcription	NHEK	skin
23	chr15:41700800-41707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:41700800-41707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:41701000-41708000	Weak transcription	Lung	lung
26	chr15:41701600-41702000	Enhancers	Primary hematopoietic stem cells	blood
27	chr15:41701600-41702400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr15:41701600-41702400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:41701600-41702400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:41701600-41702400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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