Variant report

Variant	rs1561998
Chromosome Location	chr18:9478293-9478294
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9474528..9476990-chr18:9477133..9478956,2	K562	blood:
2	chr18:9476151..9478353-chr18:9485460..9487930,2	MCF-7	breast:
3	chr18:9471240..9474381-chr18:9476825..9479081,3	K562	blood:

Variant related genes	Relation type
ENSG00000273335	Chromatin interaction
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10853380	0.87[CHB][hapmap]
rs10898	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2061692	0.83[CHB][hapmap]
rs2241943	0.87[CHB][hapmap]
rs328996	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329005	0.81[ASN][1000 genomes]
rs329006	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329007	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329012	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs396650	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7235585	0.87[CHB][hapmap]
rs7504852	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8092935	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8098663	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9807644	0.87[AFR][1000 genomes];1.00[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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1561998	C18orf1	cis	cerebellum	SCAN
rs1561998	SPIRE1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9476400-9478400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:9476600-9478400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:9476600-9478400	Weak transcription	Aorta	Aorta
4	chr18:9476600-9478400	Weak transcription	Gastric	stomach
5	chr18:9476600-9478400	Weak transcription	Lung	lung
6	chr18:9476600-9481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:9476600-9481800	Weak transcription	Pancreas	Pancrea
8	chr18:9476600-9484200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr18:9476800-9478400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr18:9476800-9478400	Weak transcription	Colonic Mucosa	Colon
11	chr18:9476800-9478400	Weak transcription	Ovary	ovary
12	chr18:9476800-9478600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr18:9476800-9479600	Weak transcription	HSMMtube	muscle
14	chr18:9476800-9480400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr18:9476800-9481200	Weak transcription	Right Atrium	heart
16	chr18:9476800-9482400	Weak transcription	Brain Anterior Caudate	brain
17	chr18:9476800-9494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:9476800-9496000	Weak transcription	Stomach Mucosa	stomach
19	chr18:9477000-9478400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr18:9477000-9478400	Weak transcription	Fetal Intestine Large	intestine
21	chr18:9477000-9478400	Weak transcription	Fetal Intestine Small	intestine
22	chr18:9477000-9478400	Weak transcription	NHLF	lung
23	chr18:9477000-9478600	Enhancers	Placenta	Placenta
24	chr18:9477000-9479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr18:9477000-9480000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr18:9477000-9481400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr18:9477000-9482400	Weak transcription	Primary T cells from cord blood	blood
28	chr18:9477000-9482400	Weak transcription	Right Ventricle	heart
29	chr18:9477000-9482800	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:9477000-9483600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:9477000-9485400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr18:9477000-9486000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr18:9477000-9489800	Weak transcription	HUVEC	blood vessel
34	chr18:9477000-9514000	Weak transcription	NH-A	brain
35	chr18:9477200-9478400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr18:9477200-9478400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr18:9477200-9478400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:9477200-9478400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr18:9477200-9478400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr18:9477200-9478400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr18:9477200-9478400	Weak transcription	Esophagus	oesophagus
42	chr18:9477200-9478400	Weak transcription	Fetal Brain Female	brain
43	chr18:9477200-9478400	Weak transcription	Left Ventricle	heart
44	chr18:9477200-9478400	Weak transcription	Spleen	Spleen
45	chr18:9477200-9481800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr18:9477200-9482000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr18:9477200-9482000	Weak transcription	Osteobl	bone
48	chr18:9477200-9482400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr18:9477200-9482400	Weak transcription	Psoas Muscle	Psoas
50	chr18:9477200-9482400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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