Variant report

Variant	rs7219320
Chromosome Location	chr17:17880877-17880878
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	chr17:17879637..17881844-chr17:17882688..17884595,2	MCF-7	breast:

Extended variants
information (count: 165 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10048206	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1052299	0.88[MEX][hapmap]
rs11078400	0.80[GIH][hapmap];0.92[MEX][hapmap]
rs11078404	0.81[EUR][1000 genomes]
rs11078405	0.81[EUR][1000 genomes]
rs11078406	0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes]
rs11078407	0.82[EUR][1000 genomes]
rs11078408	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11078409	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11650021	0.81[ASN][1000 genomes]
rs11650649	0.84[MEX][hapmap]
rs11656840	0.82[EUR][1000 genomes]
rs11657423	0.80[MEX][hapmap]
rs11869491	0.80[EUR][1000 genomes]
rs11869536	0.82[EUR][1000 genomes]
rs11870660	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871231	0.81[EUR][1000 genomes]
rs11871899	0.81[EUR][1000 genomes]
rs12150369	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12452219	0.80[EUR][1000 genomes]
rs12452254	0.81[EUR][1000 genomes]
rs12600546	0.83[EUR][1000 genomes]
rs12603148	0.82[EUR][1000 genomes]
rs12939020	0.81[ASN][1000 genomes]
rs12941039	0.84[MEX][hapmap]
rs16960744	0.92[MEX][hapmap]
rs1889018	0.80[MEX][hapmap]
rs2350977	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap]
rs28428991	0.82[EUR][1000 genomes]
rs28537385	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2955354	0.81[CEU][hapmap]
rs2955355	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs2955356	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs2955357	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs2955358	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs2955359	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2955370	0.81[CEU][hapmap]
rs2955372	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2955377	0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2955378	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs2955380	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2955383	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2955384	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2955385	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs3183702	0.89[CHD][hapmap];0.88[MEX][hapmap]
rs3744115	0.88[MEX][hapmap]
rs4072738	0.81[EUR][1000 genomes]
rs4072739	0.86[LWK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4077198	0.82[EUR][1000 genomes]
rs4077828	0.82[EUR][1000 genomes]
rs4244602	0.81[EUR][1000 genomes]
rs4257260	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4299203	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4341796	0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4343339	0.82[EUR][1000 genomes]
rs4365348	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4368210	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4413022	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4414547	0.82[EUR][1000 genomes]
rs4426402	0.81[GIH][hapmap]
rs4459604	0.82[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4470201	0.82[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes]
rs4471742	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4506969	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4534911	0.82[EUR][1000 genomes]
rs4553680	0.82[EUR][1000 genomes]
rs4584886	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4616340	0.82[EUR][1000 genomes]
rs4643387	0.81[ASN][1000 genomes]
rs4924822	0.92[MEX][hapmap]
rs4924823	0.80[GIH][hapmap];0.92[MEX][hapmap]
rs4924832	0.82[CEU][hapmap];0.90[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925119	0.88[MEX][hapmap]
rs4925120	0.92[MEX][hapmap]
rs4925123	0.84[MEX][hapmap]
rs4925125	0.83[GIH][hapmap];0.92[MEX][hapmap]
rs4925126	0.83[GIH][hapmap];0.92[MEX][hapmap]
rs4925129	0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4925130	0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs4925133	0.84[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4925136	0.81[ASN][1000 genomes]
rs5002487	0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs57728924	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59304093	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62064156	0.81[EUR][1000 genomes]
rs62064158	0.83[EUR][1000 genomes]
rs62072048	0.81[EUR][1000 genomes]
rs62072050	0.83[EUR][1000 genomes]
rs6502622	0.82[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs6502624	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes]
rs6502626	0.82[EUR][1000 genomes]
rs6502627	0.82[EUR][1000 genomes]
rs6502631	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6502632	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6502636	0.80[CEU][hapmap]
rs66531105	0.82[EUR][1000 genomes]
rs67253360	0.82[EUR][1000 genomes]
rs7207395	0.81[EUR][1000 genomes]
rs7207821	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7209003	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7210400	0.81[ASN][1000 genomes]
rs7211714	0.81[GIH][hapmap]
rs7212167	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7212447	0.81[GIH][hapmap]
rs7213225	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes]
rs7214002	0.82[EUR][1000 genomes]
rs7214536	0.82[EUR][1000 genomes]
rs7215524	0.82[EUR][1000 genomes]
rs721669	0.81[CEU][hapmap]
rs7219324	0.80[MEX][hapmap];0.93[TSI][hapmap]
rs7222480	0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs7223696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7224047	0.80[EUR][1000 genomes]
rs7359509	0.80[MEX][hapmap]
rs7406982	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7501812	0.80[MEX][hapmap]
rs7503334	0.84[MEX][hapmap]
rs8065416	0.94[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs8065563	0.84[MEX][hapmap]
rs8065970	0.82[EUR][1000 genomes]
rs8066982	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs8068175	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8068820	0.83[EUR][1000 genomes]
rs8069811	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8070128	0.84[MEX][hapmap]
rs8070722	0.81[EUR][1000 genomes]
rs8070748	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs8071238	0.82[AMR][1000 genomes]
rs8073001	0.88[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes]
rs8075189	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8078105	0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs8078138	0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs8078583	0.81[EUR][1000 genomes]
rs8079321	0.80[GIH][hapmap];0.92[MEX][hapmap]
rs8080061	0.80[GIH][hapmap];0.92[MEX][hapmap]
rs8080602	0.82[CEU][hapmap]
rs8080823	0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8082590	0.81[ASN][1000 genomes]
rs950966	0.84[MEX][hapmap]
rs9635697	0.82[EUR][1000 genomes]
rs9635698	0.81[EUR][1000 genomes]
rs9890341	0.82[EUR][1000 genomes]
rs9896837	0.82[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs9897761	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9899355	0.80[MEX][hapmap];0.93[TSI][hapmap]
rs9899634	0.80[MEX][hapmap]
rs9902941	0.84[MEX][hapmap]
rs9904163	0.82[EUR][1000 genomes]
rs9905284	0.82[EUR][1000 genomes]
rs9907246	0.84[MEX][hapmap]
rs9907287	0.80[GIH][hapmap];0.92[MEX][hapmap]
rs9908832	0.82[EUR][1000 genomes]
rs9911850	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9912096	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9912895	0.82[ASW][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs9913277	0.82[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9913724	0.81[EUR][1000 genomes]
rs9914127	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9915248	0.84[MEX][hapmap]

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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7219320	TOM1L2	cis	parietal	SCAN
rs7219320	C17orf39	cis	cerebellum	SCAN
rs7219320	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17881600	Weak transcription	Spleen	Spleen
2	chr17:17876400-17884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:17876400-17888600	Weak transcription	Lung	lung
4	chr17:17876400-17903200	Weak transcription	Gastric	stomach
5	chr17:17876600-17883400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr17:17876600-17884800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
8	chr17:17876800-17882200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr17:17876800-17883000	Weak transcription	Stomach Mucosa	stomach
10	chr17:17876800-17884400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr17:17876800-17884600	Weak transcription	Brain Angular Gyrus	brain
12	chr17:17876800-17884600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:17876800-17891800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
15	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:17877000-17881400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:17877000-17882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:17877000-17886400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:17877000-17886400	Weak transcription	NHEK	skin
20	chr17:17877000-17887000	Weak transcription	Brain Anterior Caudate	brain
21	chr17:17877000-17888000	Weak transcription	Ovary	ovary
22	chr17:17877000-17891000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:17877000-17891800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr17:17877000-17900000	Weak transcription	Fetal Intestine Small	intestine
25	chr17:17877200-17881800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr17:17877200-17891200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr17:17877200-17891400	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:17877600-17893200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:17879400-17882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:17879600-17883200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:17879800-17881600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:17880000-17885000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:17880200-17881800	Strong transcription	Pancreas	Pancrea
34	chr17:17880200-17882200	Weak transcription	Primary B cells from cord blood	blood
35	chr17:17880200-17883400	Strong transcription	Fetal Stomach	stomach
36	chr17:17880400-17882000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr17:17880600-17881000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:17880600-17881600	Enhancers	Placenta	Placenta
39	chr17:17880800-17881200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr17:17880800-17881600	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links