Variant report

Variant	rs3181369
Chromosome Location	chr9:117665866-117665867
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	chr9:117660259..117663236-chr9:117664218..117666178,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1006025	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1006026	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1006027	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10081728	0.91[ASN][1000 genomes]
rs10817682	0.83[EUR][1000 genomes]
rs10817683	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10817684	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10817685	0.81[ASN][1000 genomes]
rs10982445	0.81[EUR][1000 genomes]
rs10982449	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982451	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982453	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10982454	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10982455	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10982456	0.81[EUR][1000 genomes]
rs1126711	0.81[CEU][hapmap];0.84[GIH][hapmap];0.85[EUR][1000 genomes]
rs12337739	0.84[EUR][1000 genomes]
rs12338765	0.83[EUR][1000 genomes]
rs12347977	0.83[EUR][1000 genomes]
rs12352646	0.83[EUR][1000 genomes]
rs1322054	0.84[EUR][1000 genomes]
rs1322056	0.83[EUR][1000 genomes]
rs1322058	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1322059	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1322060	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs1322067	0.84[EUR][1000 genomes]
rs1407309	0.81[EUR][1000 genomes]
rs1555456	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17292087	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075534	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181033	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181036	0.82[EUR][1000 genomes]
rs2208640	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295800	0.84[EUR][1000 genomes]
rs2418324	0.80[EUR][1000 genomes]
rs2418325	0.81[EUR][1000 genomes]
rs2974	0.83[EUR][1000 genomes]
rs3181195	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181197	0.83[EUR][1000 genomes]
rs3181200	0.84[EUR][1000 genomes]
rs3181201	0.84[EUR][1000 genomes]
rs3181202	0.84[EUR][1000 genomes]
rs3181363	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181364	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181365	0.84[EUR][1000 genomes]
rs3181366	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181367	0.81[GIH][hapmap];0.84[EUR][1000 genomes]
rs3181368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181370	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181372	0.84[EUR][1000 genomes]
rs3181374	0.82[GIH][hapmap];0.85[EUR][1000 genomes]
rs3789879	0.83[EUR][1000 genomes]
rs4978611	0.83[EUR][1000 genomes]
rs4979470	0.81[EUR][1000 genomes]
rs4979471	0.82[EUR][1000 genomes]
rs4979472	0.81[EUR][1000 genomes]
rs4979473	0.91[ASN][1000 genomes]
rs6478117	0.83[EUR][1000 genomes]
rs7025577	0.82[EUR][1000 genomes]
rs7028578	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7030090	0.84[EUR][1000 genomes]
rs7032773	0.81[EUR][1000 genomes]
rs7036962	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7037640	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726656	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs726657	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs7858603	0.84[EUR][1000 genomes]
rs7872878	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927374	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3181369	ASTN2	cis	cerebellum	SCAN
rs3181369	KIAA1958	cis	parietal	SCAN
rs3181369	SNORA70C	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:117658400-117667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:117658600-117669200	Weak transcription	Fetal Stomach	stomach
4	chr9:117661800-117669800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:117662200-117676200	Weak transcription	Gastric	stomach
6	chr9:117662800-117666800	Weak transcription	Adipose Nuclei	Adipose
7	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
8	chr9:117663000-117668600	Weak transcription	Placenta	Placenta
9	chr9:117663000-117669200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:117663200-117666000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr9:117663200-117666800	Genic enhancers	Dnd41	blood
12	chr9:117663200-117669000	Strong transcription	Primary B cells from cord blood	blood
13	chr9:117663400-117666600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:117663600-117666200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr9:117663600-117667400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:117663600-117668200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:117663600-117669000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:117663800-117666600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr9:117664000-117670200	Weak transcription	HSMMtube	muscle
22	chr9:117664400-117667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr9:117664400-117668200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:117664400-117670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:117664600-117666600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:117664600-117668600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:117664800-117666000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:117664800-117666400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:117664800-117669200	Strong transcription	Thymus	Thymus
30	chr9:117665000-117666000	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr9:117665000-117666000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:117665000-117666600	Strong transcription	Fetal Thymus	thymus
33	chr9:117665200-117666000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
34	chr9:117665200-117666000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:117665200-117666000	Enhancers	Fetal Intestine Large	intestine
36	chr9:117665200-117666600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:117665400-117666400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:117665400-117667400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:117665400-117668600	Weak transcription	HUVEC	blood vessel
40	chr9:117665400-117670200	Weak transcription	Osteobl	bone
41	chr9:117665400-117670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:117665600-117666800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr9:117665600-117667200	Weak transcription	Fetal Intestine Small	intestine
44	chr9:117665600-117667400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:117665600-117667600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr9:117665600-117669200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:117665600-117669400	Weak transcription	HSMM	muscle
48	chr9:117665600-117671000	Weak transcription	NHLF	lung
49	chr9:117665800-117666600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:117665800-117667000	Weak transcription	NHDF-Ad	bronchial

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