Variant report

Variant	rs2290449
Chromosome Location	chr2:33442549-33442550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10205739	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10495783	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs10495784	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124309	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs11124310	0.87[ASN][1000 genomes]
rs11681694	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12611532	0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs13021881	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1377945	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1377946	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1377947	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454376	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454378	0.83[ASN][1000 genomes]
rs1454379	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17567417	0.86[CHB][hapmap]
rs17568051	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17640469	0.92[CEU][hapmap]
rs17641115	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17641180	0.81[CHB][hapmap]
rs17641906	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs17642074	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs1869542	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061026	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2061027	0.81[CHB][hapmap]
rs2290448	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs2367623	0.81[CHB][hapmap]
rs2367624	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4542826	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4670184	0.81[EUR][1000 genomes]
rs4670225	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs4670307	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.80[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670313	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670857	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.81[YRI][hapmap]
rs4670860	0.82[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs4671010	0.81[CHB][hapmap]
rs4671016	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671024	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs4671035	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs55957962	0.90[AFR][1000 genomes]
rs56163907	0.86[ASN][1000 genomes]
rs62146704	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62146732	0.87[ASN][1000 genomes]
rs6543691	0.92[CEU][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs6543698	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs6705772	0.85[CHB][hapmap]
rs6707911	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6707962	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap]
rs6708836	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs6712473	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap]
rs6720185	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap]
rs6726760	0.96[ASN][1000 genomes]
rs6728094	0.87[GIH][hapmap];0.80[LWK][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap]
rs6743685	0.82[JPT][hapmap]
rs6750739	0.84[AMR][1000 genomes]
rs6751657	0.82[CEU][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.81[YRI][hapmap]
rs7423390	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7571401	0.89[CEU][hapmap];0.88[YRI][hapmap]
rs7580348	0.81[CHB][hapmap]
rs7608222	0.87[ASN][1000 genomes]
rs7608535	0.87[ASN][1000 genomes]
rs9308931	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs961239	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs964702	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs964703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs996102	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs996103	0.81[CHB][hapmap]

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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290449	FOXH1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
3	chr2:33435800-33444400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:33436600-33444200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:33436800-33443800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:33436800-33455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:33437200-33443400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:33437400-33444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:33437800-33444400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:33437800-33444600	Weak transcription	Hela-S3	cervix
11	chr2:33437800-33445200	Weak transcription	Fetal Kidney	kidney
12	chr2:33438000-33443000	Enhancers	A549	lung
13	chr2:33439200-33442800	Enhancers	Left Ventricle	heart
14	chr2:33439600-33442800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:33439800-33442800	Enhancers	Osteobl	bone
16	chr2:33439800-33444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:33440000-33442800	Enhancers	NHEK	skin
18	chr2:33440000-33444400	Weak transcription	K562	blood
19	chr2:33440400-33446000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:33440800-33447000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:33441000-33442800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:33441400-33442800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:33441400-33442800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:33441600-33442600	Enhancers	Fetal Muscle Leg	muscle
25	chr2:33441600-33442600	Enhancers	Ovary	ovary
26	chr2:33441600-33442600	Enhancers	Right Ventricle	heart
27	chr2:33441600-33442800	Enhancers	Liver	Liver
28	chr2:33441600-33442800	Enhancers	Fetal Lung	lung
29	chr2:33441600-33442800	Enhancers	Psoas Muscle	Psoas
30	chr2:33441600-33442800	Enhancers	Right Atrium	heart
31	chr2:33441600-33443000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:33441800-33443600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:33442000-33442600	Enhancers	Stomach Smooth Muscle	stomach
34	chr2:33442000-33442800	Enhancers	NHLF	lung
35	chr2:33442000-33444400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:33442000-33445000	Weak transcription	HSMMtube	muscle
37	chr2:33442000-33445600	Weak transcription	Aorta	Aorta
38	chr2:33442200-33443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:33442200-33444200	Weak transcription	HUVEC	blood vessel
40	chr2:33442200-33444400	Weak transcription	NH-A	brain
41	chr2:33442200-33444600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:33442200-33444600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:33442200-33444600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:33442200-33444800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:33442200-33444800	Weak transcription	Fetal Heart	heart
46	chr2:33442200-33445000	Weak transcription	HSMM	muscle
47	chr2:33442200-33445600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:33442200-33447000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:33442200-33447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:33442400-33444600	Weak transcription	NHDF-Ad	bronchial

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