Variant report

Variant	rs34229934
Chromosome Location	chr18:12599765-12599766
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12598216..12599917-chr18:12611119..12613294,2	MCF-7	breast:
2	chr18:12594070..12599084-chr18:12599553..12605396,7	K562	blood:
3	chr18:12407681..12409442-chr18:12599712..12601429,2	K562	blood:

Variant related genes	Relation type
ENSG00000141391	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1105748	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959459	1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.81[AFR][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];0.91[AMR][1000 genomes];0.91[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];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	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];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs35532404	1.00[ASN][1000 genomes]
rs35612342	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[ASN][1000 genomes]
rs35643117	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35686128	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	0.81[AFR][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[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];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[ASN][1000 genomes]
rs71363149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34229934	RP11-861E21.2	cis	Thyroid	GTEx
rs34229934	SLMO1	cis	Artery Tibial	GTEx
rs34229934	RP11-861E21.1	cis	Artery Tibial	GTEx
rs34229934	SPIRE1	cis	Thyroid	GTEx
rs34229934	AP001029.1	cis	Artery Tibial	GTEx
rs34229934	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12594600-12600400	Enhancers	HepG2	liver
2	chr18:12595400-12600400	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr18:12595600-12600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:12595600-12600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr18:12595600-12600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr18:12595800-12600600	Enhancers	HMEC	breast
7	chr18:12596600-12600000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr18:12596800-12599800	Enhancers	Fetal Brain Female	brain
9	chr18:12596800-12600400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr18:12596800-12600400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:12596800-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr18:12596800-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:12596800-12600600	Enhancers	NHDF-Ad	bronchial
14	chr18:12596800-12600600	Enhancers	NHEK	skin
15	chr18:12597000-12600200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr18:12597000-12605800	Weak transcription	Gastric	stomach
17	chr18:12597000-12605800	Weak transcription	K562	blood
18	chr18:12597000-12606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:12597200-12600000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr18:12597200-12600400	Enhancers	NHLF	lung
21	chr18:12597400-12599800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr18:12597400-12600400	Enhancers	Primary T cells from cord blood	blood
23	chr18:12597600-12600400	Enhancers	HSMM	muscle
24	chr18:12597800-12610800	Weak transcription	Right Ventricle	heart
25	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
26	chr18:12598000-12600000	Enhancers	A549	lung
27	chr18:12598000-12600400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr18:12598000-12600400	Enhancers	Osteobl	bone
29	chr18:12598000-12600600	Enhancers	HSMMtube	muscle
30	chr18:12598000-12601800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr18:12598000-12601800	Weak transcription	Brain Hippocampus Middle	brain
32	chr18:12598000-12601800	Weak transcription	Fetal Thymus	thymus
33	chr18:12598000-12606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:12598000-12607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr18:12598000-12607200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr18:12598000-12610000	Weak transcription	Lung	lung
37	chr18:12598200-12600400	Enhancers	Primary hematopoietic stem cells	blood
38	chr18:12598200-12606800	Weak transcription	Brain Anterior Caudate	brain
39	chr18:12598600-12600000	Enhancers	Pancreas	Pancrea
40	chr18:12598600-12608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr18:12598800-12599800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:12598800-12600400	Enhancers	Hela-S3	cervix
43	chr18:12598800-12600400	Enhancers	HUVEC	blood vessel
44	chr18:12598800-12600600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr18:12598800-12606000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr18:12598800-12606000	Weak transcription	Left Ventricle	heart
47	chr18:12598800-12606800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr18:12598800-12607000	Weak transcription	Brain Angular Gyrus	brain
49	chr18:12598800-12609000	Weak transcription	Right Atrium	heart
50	chr18:12599000-12600400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links