Variant report

Variant	rs2349098
Chromosome Location	chr2:48794283-48794284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48788958..48790786-chr2:48792304..48795204,2	K562	blood:
2	chr2:48793447..48794436-chr2:48816095..48816687,2	K562	blood:
3	chr2:48793384..48794350-chr2:48816086..48816820,5	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10495953	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125176	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11676150	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11678306	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11680574	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11681276	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11681426	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11681868	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11683611	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693429	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693559	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11693691	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475789	0.89[ASN][1000 genomes]
rs12990079	0.90[CHB][hapmap];0.91[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12992755	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12992870	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999304	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13010692	0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13011288	0.87[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs13014112	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13016899	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13025488	0.80[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13027618	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13030948	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13031184	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13034063	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13034951	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17037412	0.87[CHB][hapmap]
rs17039250	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996970	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2103112	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2177489	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293270	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293271	0.91[ASN][1000 genomes]
rs2293272	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293274	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882084	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3749142	0.87[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.90[ASN][1000 genomes]
rs3749144	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749145	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792234	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.99[ASN][1000 genomes]
rs3792235	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792236	0.82[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792237	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792238	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3828340	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4566410	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953593	0.82[EUR][1000 genomes]
rs55641971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55700200	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55858189	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56111874	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62135201	0.83[ASN][1000 genomes]
rs62135230	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62135231	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62135232	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62135233	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62135236	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545048	1.00[ASN][1000 genomes]
rs66888174	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709043	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710565	0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6712592	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712724	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6716291	0.87[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs6722556	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727929	0.94[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6729860	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6732365	0.82[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6737732	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6741341	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741677	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742725	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757847	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6761796	0.90[ASN][1000 genomes]
rs940389	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1000419	chr2:48766957-48795327	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2349098	STON1-GTF2A1L	cis	cerebellum	SCAN
rs2349098	FOXN2	cis	parietal	SCAN
rs2349098	STON1-GTF2A1L	cis	lung	GTEx
rs2349098	STON1	cis	Esophagus Muscularis	GTEx
rs2349098	RHOQ	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:48767200-48807800	Weak transcription	Aorta	Aorta
3	chr2:48773000-48808800	Weak transcription	Right Ventricle	heart
4	chr2:48777200-48807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:48779400-48800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:48787800-48802200	Weak transcription	Esophagus	oesophagus
7	chr2:48788200-48794600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:48788200-48795200	Weak transcription	Right Atrium	heart
9	chr2:48788200-48798200	Weak transcription	Lung	lung
10	chr2:48788400-48795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:48788400-48795000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:48788400-48799400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:48788400-48804600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:48788600-48812000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:48790000-48800000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:48790600-48794800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:48793000-48795600	Enhancers	Colon Smooth Muscle	Colon
18	chr2:48793200-48796000	Enhancers	Fetal Lung	lung
19	chr2:48793600-48794400	Enhancers	Ovary	ovary
20	chr2:48793600-48795400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:48793600-48795600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:48793600-48795600	Enhancers	Fetal Stomach	stomach
23	chr2:48793600-48796200	Enhancers	Fetal Kidney	kidney
24	chr2:48793600-48796200	Enhancers	Placenta	Placenta
25	chr2:48793800-48794400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:48793800-48794400	Enhancers	Brain Anterior Caudate	brain
27	chr2:48793800-48794400	Enhancers	Fetal Intestine Large	intestine
28	chr2:48793800-48794400	Enhancers	NHDF-Ad	bronchial
29	chr2:48793800-48794400	Flanking Active TSS	Osteobl	bone
30	chr2:48793800-48795200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:48793800-48795400	Enhancers	Brain Hippocampus Middle	brain
32	chr2:48793800-48795600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:48793800-48795600	Enhancers	Fetal Heart	heart
34	chr2:48793800-48795800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:48793800-48795800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:48793800-48796000	Enhancers	Adipose Nuclei	Adipose
37	chr2:48793800-48796000	Enhancers	Fetal Muscle Leg	muscle
38	chr2:48793800-48796000	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:48794000-48794400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:48794000-48794400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:48794000-48794400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:48794000-48794400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr2:48794000-48794400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:48794000-48794400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:48794000-48794600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:48794000-48795200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr2:48794000-48795400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:48794000-48796000	Enhancers	Brain Substantia Nigra	brain
49	chr2:48794000-48807800	Weak transcription	Psoas Muscle	Psoas
50	chr2:48794200-48794600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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