Variant report

Variant	rs7166073
Chromosome Location	chr15:51268452-51268453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51265611..51268548-chr15:51273285..51275187,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11070825	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11854729	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11856129	0.85[EUR][1000 genomes]
rs11857981	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12324214	0.93[CEU][hapmap];0.88[TSI][hapmap]
rs12324583	0.93[CEU][hapmap]
rs12898402	0.93[CEU][hapmap]
rs12899397	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12901860	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12902050	0.81[TSI][hapmap]
rs12902196	0.84[EUR][1000 genomes]
rs12904155	0.93[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12906205	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12907367	0.93[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909780	0.85[EUR][1000 genomes]
rs12911270	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs12913094	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12916334	0.84[EUR][1000 genomes]
rs1438926	0.93[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs16953045	0.93[CEU][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17521467	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17521789	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17521919	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17599863	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17599974	0.92[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1904432	0.92[CEU][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1912097	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2083254	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2306333	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28366661	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28430533	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28642856	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34874493	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35114758	0.89[EUR][1000 genomes]
rs35134521	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35416047	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35439349	0.84[EUR][1000 genomes]
rs35655196	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3759806	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848133	0.93[CEU][hapmap];0.88[TSI][hapmap]
rs3848134	0.93[CEU][hapmap]
rs4134038	0.84[EUR][1000 genomes]
rs58661036	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71426066	0.84[EUR][1000 genomes]
rs71471522	0.84[EUR][1000 genomes]
rs71471523	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71471584	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71471585	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71471587	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7162325	0.93[CEU][hapmap]
rs7162631	0.93[CEU][hapmap]
rs7165920	0.86[EUR][1000 genomes]
rs7166600	0.84[EUR][1000 genomes]
rs7170009	0.93[CEU][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7170937	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs7175024	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7179321	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7179865	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs8032236	0.88[EUR][1000 genomes]
rs8032550	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032866	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8033351	0.93[CEU][hapmap]
rs8034718	0.93[CEU][hapmap]
rs9302158	0.93[CEU][hapmap];0.88[TSI][hapmap]
rs9806654	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7166073	TRPM7	cis	cerebellum	SCAN
rs7166073	DUOXA2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
3	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:51252400-51283800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:51257600-51272800	Weak transcription	Pancreas	Pancrea
6	chr15:51261000-51269200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:51261600-51272800	Weak transcription	Colonic Mucosa	Colon
8	chr15:51261600-51295600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:51261600-51298200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:51263000-51304800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:51263200-51276000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:51263400-51281000	Weak transcription	Fetal Heart	heart
13	chr15:51263600-51287200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:51263600-51293600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51263600-51296400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:51263600-51297800	Weak transcription	NHLF	lung
17	chr15:51263600-51299200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:51263600-51300200	Weak transcription	Small Intestine	intestine
19	chr15:51263600-51301200	Weak transcription	HepG2	liver
20	chr15:51263600-51303000	Weak transcription	HUVEC	blood vessel
21	chr15:51263800-51269400	Weak transcription	Psoas Muscle	Psoas
22	chr15:51263800-51272600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:51263800-51275400	Weak transcription	NH-A	brain
24	chr15:51263800-51296200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:51263800-51296600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:51263800-51300400	Weak transcription	Right Ventricle	heart
27	chr15:51264400-51269400	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:51264400-51271000	Weak transcription	Osteobl	bone
29	chr15:51264400-51283200	Weak transcription	Brain Substantia Nigra	brain
30	chr15:51264400-51294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:51264600-51296600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:51265000-51270800	Weak transcription	Brain Anterior Caudate	brain
33	chr15:51265000-51272800	Weak transcription	Thymus	Thymus
34	chr15:51265000-51275800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:51265200-51270600	Weak transcription	Left Ventricle	heart
36	chr15:51265200-51272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:51265200-51272600	Weak transcription	NHEK	skin
38	chr15:51265200-51272800	Weak transcription	Aorta	Aorta
39	chr15:51265200-51272800	Weak transcription	Esophagus	oesophagus
40	chr15:51265200-51272800	Weak transcription	Lung	lung
41	chr15:51265200-51272800	Weak transcription	Ovary	ovary
42	chr15:51265200-51272800	Weak transcription	Spleen	Spleen
43	chr15:51265200-51273000	Weak transcription	Fetal Thymus	thymus
44	chr15:51265200-51274000	Strong transcription	Primary B cells from cord blood	blood
45	chr15:51265200-51275400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:51265200-51276200	Weak transcription	A549	lung
47	chr15:51265200-51292600	Weak transcription	Brain Angular Gyrus	brain
48	chr15:51265200-51296400	Weak transcription	Brain Germinal Matrix	brain
49	chr15:51265200-51302400	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:51265200-51315600	Weak transcription	Gastric	stomach

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