Variant report

Variant	rs2295800
Chromosome Location	chr9:117664211-117664212
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	chr9:117653018..117655628-chr9:117662655..117665359,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DEC1-7	chr9:117664203-117664893	NONHSAT134406

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1006025	0.82[EUR][1000 genomes]
rs1006026	0.95[EUR][1000 genomes]
rs1006027	0.82[EUR][1000 genomes]
rs10081728	0.85[EUR][1000 genomes]
rs10817682	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817683	0.95[EUR][1000 genomes]
rs10817685	0.81[EUR][1000 genomes]
rs10982445	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10982449	0.83[EUR][1000 genomes]
rs10982450	0.84[EUR][1000 genomes]
rs10982451	0.84[EUR][1000 genomes]
rs10982453	0.83[EUR][1000 genomes]
rs10982454	0.83[EUR][1000 genomes]
rs10982455	0.83[EUR][1000 genomes]
rs10982456	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1126711	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12337739	0.96[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12338765	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12347977	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12352646	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1322054	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1322056	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1322058	0.83[EUR][1000 genomes]
rs1322060	0.89[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1322067	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407309	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17292087	0.85[EUR][1000 genomes]
rs2075533	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2181036	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208640	0.84[EUR][1000 genomes]
rs2418324	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418325	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181195	0.86[GIH][hapmap];0.85[EUR][1000 genomes]
rs3181197	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3181200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181201	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181348	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3181363	0.84[EUR][1000 genomes]
rs3181364	0.85[EUR][1000 genomes]
rs3181365	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181366	0.85[EUR][1000 genomes]
rs3181367	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181368	0.84[EUR][1000 genomes]
rs3181369	0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs3181370	0.84[EUR][1000 genomes]
rs3181371	0.84[EUR][1000 genomes]
rs3181372	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181374	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789879	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4978611	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979470	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979471	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979472	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4979473	0.86[EUR][1000 genomes]
rs5003740	0.86[ASN][1000 genomes]
rs6478117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025577	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7028578	0.84[EUR][1000 genomes]
rs7030090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032773	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7036962	0.83[EUR][1000 genomes]
rs7037640	0.84[EUR][1000 genomes]
rs726657	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7858603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7872878	0.96[EUR][1000 genomes]
rs911603	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs927373	0.83[EUR][1000 genomes]
rs927374	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs927375	0.88[AMR][1000 genomes];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
rs2295800	ASTN2	cis	cerebellum	SCAN
rs2295800	KIAA1958	cis	parietal	SCAN
rs2295800	SNORA70C	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117655600-117664800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:117657800-117664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:117657800-117665400	Enhancers	HUVEC	blood vessel
4	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:117658200-117664600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:117658400-117665200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:117658400-117665800	Enhancers	NHDF-Ad	bronchial
8	chr9:117658400-117667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:117658600-117669200	Weak transcription	Fetal Stomach	stomach
10	chr9:117659600-117665400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:117660600-117665400	Enhancers	Osteobl	bone
12	chr9:117660600-117665600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:117661200-117665800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:117661200-117665800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:117661600-117665400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:117661800-117665600	Enhancers	HSMM	muscle
17	chr9:117661800-117665600	Enhancers	NHLF	lung
18	chr9:117661800-117669800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:117662000-117664400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:117662000-117665400	Weak transcription	Spleen	Spleen
21	chr9:117662200-117665200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:117662200-117676200	Weak transcription	Gastric	stomach
23	chr9:117662600-117665600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:117662800-117664600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:117662800-117665200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:117662800-117665200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr9:117662800-117665200	Enhancers	NH-A	brain
28	chr9:117662800-117665800	Genic enhancers	Primary T cells from cord blood	blood
29	chr9:117662800-117666800	Weak transcription	Adipose Nuclei	Adipose
30	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
31	chr9:117663000-117665200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr9:117663000-117665200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr9:117663000-117665400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:117663000-117668600	Weak transcription	Placenta	Placenta
35	chr9:117663000-117669200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:117663200-117664800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:117663200-117665200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr9:117663200-117665800	Enhancers	HMEC	breast
39	chr9:117663200-117666000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr9:117663200-117666800	Genic enhancers	Dnd41	blood
41	chr9:117663200-117669000	Strong transcription	Primary B cells from cord blood	blood
42	chr9:117663400-117664400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:117663400-117664400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:117663400-117664800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:117663400-117665000	Weak transcription	Fetal Thymus	thymus
46	chr9:117663400-117666600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:117663600-117664400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:117663600-117664600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:117663600-117665800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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