Variant report

Variant	rs694861
Chromosome Location	chr18:9632372-9632373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9631123..9633361-chr18:9636042..9638637,2	MCF-7	breast:
2	chr18:9627468..9629148-chr18:9631077..9633967,2	MCF-7	breast:
3	chr18:9615287..9617165-chr18:9631128..9633561,2	K562	blood:
4	chr18:9630794..9635395-chr18:9635739..9640579,6	MCF-7	breast:
5	chr18:9613322..9616400-chr18:9628599..9633857,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11081489	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1662885	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787165	0.90[ASN][1000 genomes]
rs1787166	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2028661	0.89[ASN][1000 genomes]
rs2028662	0.89[ASN][1000 genomes]
rs2028663	0.89[ASN][1000 genomes]
rs2289684	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2903504	0.81[EUR][1000 genomes]
rs328995	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs329002	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329004	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs329023	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35444634	0.89[ASN][1000 genomes]
rs407530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs428598	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs583306	0.89[ASN][1000 genomes]
rs586544	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs589559	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs599861	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610564	0.85[EUR][1000 genomes]
rs62088920	0.90[ASN][1000 genomes]
rs633907	0.85[CHB][hapmap]
rs638578	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667695	0.89[ASN][1000 genomes]
rs671339	0.89[ASN][1000 genomes]
rs677461	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs680478	0.89[ASN][1000 genomes]
rs681297	0.89[ASN][1000 genomes]
rs683319	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233160	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7234128	1.00[ASN][1000 genomes]
rs8090919	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807577	0.81[ASN][1000 genomes]
rs9807604	0.89[ASN][1000 genomes]
rs9807610	0.86[ASN][1000 genomes]
rs9950583	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576449	chr18:9623052-9700382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs694861	SPIRE1	cis	cerebellum	SCAN
rs694861	RP11-692N5.1	cis	Nerve Tibial	GTEx
rs694861	RP11-692N5.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9628000-9642800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr18:9630000-9633000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr18:9630600-9632400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr18:9630600-9632400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr18:9630600-9632400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr18:9630600-9632400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:9630600-9632400	Enhancers	Fetal Heart	heart
8	chr18:9630600-9632600	Enhancers	Hela-S3	cervix
9	chr18:9630800-9638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:9631000-9632400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:9631000-9637000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:9631000-9638800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr18:9631200-9632400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:9631200-9632600	Enhancers	NHLF	lung
15	chr18:9631200-9642000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr18:9631400-9632600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:9631400-9632600	Enhancers	Osteobl	bone
18	chr18:9631600-9632400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr18:9631600-9632400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:9631600-9632600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:9631800-9632400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:9631800-9632400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr18:9631800-9632400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:9631800-9632400	Enhancers	Colon Smooth Muscle	Colon
25	chr18:9631800-9632400	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr18:9631800-9632400	Enhancers	Stomach Mucosa	stomach
27	chr18:9631800-9632400	Enhancers	Stomach Smooth Muscle	stomach
28	chr18:9631800-9632400	Flanking Active TSS	A549	lung
29	chr18:9631800-9632400	Enhancers	NHEK	skin
30	chr18:9631800-9632600	Enhancers	HSMM	muscle
31	chr18:9631800-9632600	Enhancers	HUVEC	blood vessel
32	chr18:9631800-9633000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:9632000-9632400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr18:9632000-9632400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr18:9632000-9632400	Enhancers	Rectal Smooth Muscle	rectum
36	chr18:9632000-9632400	Enhancers	HMEC	breast
37	chr18:9632000-9632400	Flanking Active TSS	HSMMtube	muscle
38	chr18:9632000-9632400	Flanking Active TSS	NH-A	brain
39	chr18:9632000-9632400	Flanking Active TSS	NHDF-Ad	bronchial
40	chr18:9632000-9632600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:9632200-9632400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr18:9632200-9632400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr18:9632200-9633000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr18:9632200-9633400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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