Variant report

Variant	rs34180475
Chromosome Location	chr18:12655583-12655584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
2	chr18:12648702..12654959-chr18:12655130..12658770,8	K562	blood:
3	chr18:12543497..12545408-chr18:12653876..12656459,2	MCF-7	breast:
4	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
5	chr18:12649857..12654959-chr18:12655130..12658770,11	K562	blood:
6	chr18:12654302..12656873-chr18:12657659..12659911,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1105748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971000	1.00[ASN][1000 genomes]
rs17524639	1.00[ASN][1000 genomes]
rs17525318	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34183067	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	1.00[ASN][1000 genomes]
rs34229934	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34469203	1.00[ASN][1000 genomes]
rs34503700	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34512782	1.00[ASN][1000 genomes]
rs34737110	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35643117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35686128	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71351482	1.00[ASN][1000 genomes]
rs71351484	1.00[ASN][1000 genomes]
rs71351485	1.00[ASN][1000 genomes]
rs71351491	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv576497	chr18:12650900-12658293	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv576498	chr18:12650900-12658436	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34180475	SPIRE1	cis	Thyroid	GTEx
rs34180475	RP11-861E21.1	cis	Artery Tibial	GTEx
rs34180475	RP11-861E21.2	cis	Thyroid	GTEx
rs34180475	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL
rs34180475	SLMO1	cis	Artery Tibial	GTEx
rs34180475	AP001029.1	cis	Artery Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
2	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:12646400-12656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:12646400-12656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr18:12646400-12657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:12648000-12656800	Weak transcription	Left Ventricle	heart
8	chr18:12648400-12656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12648600-12655800	Weak transcription	Fetal Muscle Leg	muscle
10	chr18:12648600-12656800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr18:12653000-12655800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr18:12653200-12656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:12653200-12656600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:12653200-12656600	Weak transcription	Right Atrium	heart
15	chr18:12653200-12656600	Weak transcription	Right Ventricle	heart
16	chr18:12653200-12656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12653200-12656800	Weak transcription	Esophagus	oesophagus
18	chr18:12653200-12657000	Weak transcription	Spleen	Spleen
19	chr18:12653400-12655600	Weak transcription	HMEC	breast
20	chr18:12653400-12656400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr18:12653400-12656400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:12653400-12656600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr18:12653400-12656600	Weak transcription	Aorta	Aorta
24	chr18:12653400-12656600	Weak transcription	Psoas Muscle	Psoas
25	chr18:12653400-12657000	Weak transcription	Pancreas	Pancrea
26	chr18:12653400-12657000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr18:12653600-12655600	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:12653600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr18:12653600-12655800	Weak transcription	HSMM	muscle
30	chr18:12653600-12656200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr18:12653600-12656400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:12653600-12656400	Weak transcription	A549	lung
33	chr18:12653600-12656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr18:12653600-12656600	Weak transcription	Liver	Liver
35	chr18:12653600-12656600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:12653800-12655600	Weak transcription	NHLF	lung
37	chr18:12653800-12655600	Weak transcription	Osteobl	bone
38	chr18:12653800-12655800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:12653800-12656600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr18:12653800-12656800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr18:12653800-12656800	Weak transcription	Lung	lung
42	chr18:12653800-12656800	Weak transcription	Ovary	ovary
43	chr18:12653800-12670400	Weak transcription	Dnd41	blood
44	chr18:12654000-12655800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:12654000-12656400	Weak transcription	Adipose Nuclei	Adipose
46	chr18:12654000-12656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr18:12654000-12656800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr18:12654200-12655800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr18:12654200-12656000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr18:12655000-12655600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links