Variant report

Variant	rs1440154
Chromosome Location	chr3:98544866-98544867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98544275..98546874-chr3:98717004..98718969,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10433438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10511169	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10511171	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs10935518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10935542	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap]
rs11716579	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11914715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11916285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][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]
rs12203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16846347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17210963	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs17278047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs17852693	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822017	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772100	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55650073	0.92[EUR][1000 genomes]
rs55662129	0.97[EUR][1000 genomes]
rs55730510	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55988144	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56075614	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290036	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56322058	0.92[EUR][1000 genomes]
rs6440159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs73136038	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136057	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138004	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138027	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73138030	0.97[EUR][1000 genomes]
rs73138048	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138053	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138055	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138058	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138063	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73138082	0.92[EUR][1000 genomes]
rs73140009	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7614892	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7629550	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs7644946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179927	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1440154	OR5K2	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
3	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
4	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
10	chr3:98534000-98545000	Weak transcription	Ovary	ovary
11	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
16	chr3:98536200-98594200	Weak transcription	HepG2	liver
17	chr3:98536800-98545000	Weak transcription	Fetal Kidney	kidney
18	chr3:98537000-98545600	Weak transcription	HSMMtube	muscle
19	chr3:98537000-98546200	Weak transcription	Brain Anterior Caudate	brain
20	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:98537000-98592800	Weak transcription	K562	blood
22	chr3:98537400-98551200	Weak transcription	Fetal Heart	heart
23	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:98538600-98545000	Weak transcription	Fetal Lung	lung
25	chr3:98538800-98545400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:98538800-98548200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:98538800-98552200	Weak transcription	Left Ventricle	heart
28	chr3:98539400-98546400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:98540200-98545000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:98541200-98545000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:98541200-98545200	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:98541200-98552200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:98541200-98567000	Weak transcription	Liver	Liver
34	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
35	chr3:98541600-98548400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:98541800-98545600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:98541800-98546600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:98542600-98545800	Genic enhancers	Osteobl	bone
39	chr3:98542800-98551200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:98543000-98552400	Weak transcription	NHLF	lung
41	chr3:98543400-98545000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:98543400-98545200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:98543400-98546200	Weak transcription	Right Atrium	heart
44	chr3:98543400-98552400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:98543400-98552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:98543400-98552400	Weak transcription	Fetal Stomach	stomach
47	chr3:98543600-98545000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:98543600-98545000	Weak transcription	NHEK	skin
49	chr3:98543600-98545200	Strong transcription	NH-A	brain
50	chr3:98543600-98551200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links