Variant report

Variant	rs7164684
Chromosome Location	chr15:41705008-41705009
allele	G/T
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	chr15:41704958-41705122	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:41704785-41705032	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41704630..41706347-chr15:41708532..41710045,2	MCF-7	breast:

Variant related genes	Relation type
RTF1	TF binding region
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10518717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs170296	1.00[LWK][hapmap]
rs1757457	1.00[LWK][hapmap]
rs1757468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs17730888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2730056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap]
rs28377562	1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28448670	1.00[AFR][1000 genomes]
rs28456082	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28463309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs28535540	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs28555198	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs28576457	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631111	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs28661013	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.99[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	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.93[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34285452	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34665396	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924549	1.00[CHB][hapmap]
rs513280	1.00[ASN][1000 genomes]
rs55725658	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.83[EUR][1000 genomes]
rs56400990	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs7168431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][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[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs8034840	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs8038132	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041809	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	0.87[CEU][hapmap];1.00[CHB][hapmap];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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs7164684	NDUFAF1	cis	lung	GTEx
rs7164684	GPR176	cis	parietal	SCAN
rs7164684	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7164684	NDUFAF1	cis	multi-tissue	Pritchard
rs7164684	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7164684	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7164684	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7164684	ZFP106	cis	parietal	SCAN
rs7164684	OIP5-AS1	cis	Artery Tibial	GTEx
rs7164684	ITPKA	cis	lymphoblastoid	seeQTL
rs7164684	SPINT1	cis	cerebellum	SCAN
rs7164684	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs7164684	NDUFAF1	cis	cerebellum	SCAN
rs7164684	RPAP1	cis	parietal	SCAN
rs7164684	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7164684	NDUFAF1	cis	Thyroid	GTEx
rs7164684	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7164684	NDUFAF1	cis	parietal	SCAN
rs7164684	RASGRP1	cis	cerebellum	SCAN
rs7164684	NUSAP1	cis	cerebellum	SCAN
rs7164684	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7164684	NUSAP1	cis	parietal	SCAN
rs7164684	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs7164684	NDUFAF1	cis	Whole Blood	GTEx
rs7164684	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7164684	GPR176	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41695400-41707800	Weak transcription	HSMMtube	muscle
2	chr15:41695400-41708400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:41695600-41707600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:41695600-41707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:41695600-41708400	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:41697400-41707800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:41699600-41706400	Weak transcription	HepG2	liver
8	chr15:41700600-41707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:41700600-41707800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:41700800-41707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:41700800-41707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:41701000-41708000	Weak transcription	Lung	lung
13	chr15:41702000-41708200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:41702200-41707800	Weak transcription	A549	lung
15	chr15:41702200-41708400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:41702400-41707600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:41702400-41707800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:41702400-41707800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:41702400-41707800	Weak transcription	Fetal Intestine Large	intestine
20	chr15:41702400-41707800	Weak transcription	Fetal Intestine Small	intestine
21	chr15:41703200-41707600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:41703200-41707800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:41703400-41707600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:41703400-41708200	Weak transcription	Stomach Mucosa	stomach
25	chr15:41703600-41707600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:41704200-41707400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:41704200-41707600	Weak transcription	HMEC	breast
28	chr15:41704200-41707800	Weak transcription	NHEK	skin
29	chr15:41704200-41708200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:41704200-41708400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:41704600-41708200	Weak transcription	NHLF	lung
32	chr15:41705000-41705400	Enhancers	K562	blood

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