Variant report

Variant	rs12959199
Chromosome Location	chr18:12673574-12673575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12672017..12674011-chr18:12701088..12702712,2	MCF-7	breast:
2	chr18:12671690..12675080-chr18:12702112..12705449,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1105748	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs12961711	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525318	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17615801	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17615991	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[AFR][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];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	1.00[AFR][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];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35643117	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs35686128	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[ASN][1000 genomes]
rs71351485	1.00[ASN][1000 genomes]
rs71351491	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12959199	SLMO1	cis	Artery Tibial	GTEx
rs12959199	SPIRE1	cis	Thyroid	GTEx
rs12959199	CEP76	Cis_1M	lymphoblastoid	RTeQTL
rs12959199	RP11-861E21.2	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658400-12674000	Weak transcription	Spleen	Spleen
2	chr18:12658800-12674000	Weak transcription	Fetal Lung	lung
3	chr18:12658800-12674000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr18:12658800-12679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:12659000-12674000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr18:12659000-12674000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr18:12659000-12674000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:12659000-12674000	Weak transcription	Brain Angular Gyrus	brain
10	chr18:12659000-12674000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:12659000-12674000	Weak transcription	Right Ventricle	heart
12	chr18:12659000-12676600	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:12659000-12679200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr18:12659000-12679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr18:12659000-12679400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr18:12659200-12673800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:12659200-12674000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr18:12659200-12674000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr18:12659200-12674000	Weak transcription	HSMMtube	muscle
21	chr18:12659600-12674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:12659800-12679200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:12660000-12692600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:12660200-12677800	Weak transcription	HMEC	breast
25	chr18:12660400-12674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr18:12660400-12677800	Weak transcription	NHDF-Ad	bronchial
27	chr18:12660400-12679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
29	chr18:12661000-12679000	Weak transcription	HUVEC	blood vessel
30	chr18:12661800-12674000	Weak transcription	Ovary	ovary
31	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
32	chr18:12664800-12679000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:12665800-12684200	Weak transcription	Pancreas	Pancrea
34	chr18:12667000-12701600	Weak transcription	Gastric	stomach
35	chr18:12667800-12679000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr18:12668200-12675400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr18:12668400-12674200	Weak transcription	Lung	lung
38	chr18:12668400-12679200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr18:12668400-12694800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr18:12668600-12674000	Weak transcription	Primary B cells from cord blood	blood
41	chr18:12668600-12685800	Weak transcription	Brain Hippocampus Middle	brain
42	chr18:12669000-12674000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr18:12669000-12677600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr18:12669200-12674000	Weak transcription	Small Intestine	intestine
45	chr18:12669200-12694200	Weak transcription	A549	lung
46	chr18:12669800-12694200	Weak transcription	Hela-S3	cervix
47	chr18:12670000-12673800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr18:12670000-12674000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr18:12670000-12679200	Weak transcription	Esophagus	oesophagus
50	chr18:12670000-12679200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links