Variant report

Variant	rs17165582
Chromosome Location	chr7:12151786-12151787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10236588	0.99[EUR][1000 genomes]
rs10251182	0.92[ASN][1000 genomes]
rs10263550	0.92[ASN][1000 genomes]
rs10280578	0.92[ASN][1000 genomes]
rs10950383	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10950384	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11761090	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11770347	0.92[ASN][1000 genomes]
rs11771114	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773443	0.92[ASN][1000 genomes]
rs11977250	0.92[ASN][1000 genomes]
rs11977297	0.92[ASN][1000 genomes]
rs11980827	0.92[ASN][1000 genomes]
rs12699310	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12699311	0.92[ASN][1000 genomes]
rs13221968	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17592324	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17650986	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1861279	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2192732	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356053	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356055	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2356056	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35649285	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35828107	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36014865	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236267	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4236268	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4719294	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4719295	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4719296	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4721038	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4721039	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4721041	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4721042	0.90[EUR][1000 genomes]
rs6460882	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68113272	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6945990	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6952511	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6956124	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7783494	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7790585	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7797675	0.97[EUR][1000 genomes]
rs9638681	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv887614	chr7:11778424-12211198	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv830906	chr7:12001764-12177869	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1023608	chr7:12064114-12247520	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1031893	chr7:12127098-12155796	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17165582	TMEM109	cis	Cerebellum	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12150600-12151800	Active TSS	Colon Smooth Muscle	Colon
2	chr7:12150800-12151800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:12150800-12151800	Active TSS	Brain Angular Gyrus	brain
4	chr7:12150800-12151800	Active TSS	Brain Anterior Caudate	brain
5	chr7:12150800-12151800	Active TSS	Brain Cingulate Gyrus	brain
6	chr7:12150800-12151800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr7:12150800-12151800	Active TSS	Brain Substantia Nigra	brain
8	chr7:12150800-12152000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr7:12150800-12152000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:12150800-12152000	Active TSS	Brain Hippocampus Middle	brain
11	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr7:12151000-12151800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:12151000-12151800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:12151000-12151800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:12151000-12151800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
18	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:12151000-12151800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:12151000-12151800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr7:12151000-12151800	ZNF genes & repeats	Fetal Intestine Large	intestine
26	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
27	chr7:12151000-12151800	Active TSS	Fetal Kidney	kidney
28	chr7:12151000-12151800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr7:12151000-12151800	Bivalent/Poised TSS	Fetal Stomach	stomach
30	chr7:12151000-12151800	Active TSS	Osteobl	bone
31	chr7:12151000-12152000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr7:12151000-12152000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:12151000-12152000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:12151000-12152000	Active TSS	Rectal Smooth Muscle	rectum
35	chr7:12151200-12151800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:12151200-12151800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:12151200-12151800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:12151200-12151800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:12151200-12151800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr7:12151200-12151800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:12151200-12151800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:12151200-12151800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:12151200-12151800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr7:12151200-12151800	Enhancers	Gastric	stomach
45	chr7:12151200-12151800	Enhancers	Lung	lung
46	chr7:12151200-12151800	Enhancers	Spleen	Spleen
47	chr7:12151200-12152000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr7:12151200-12152000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:12151400-12151800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
50	chr7:12151400-12151800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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