Variant report

Variant	rs12464003
Chromosome Location	chr2:188129650-188129651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10177093	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10197758	0.86[EUR][1000 genomes]
rs10931281	0.85[EUR][1000 genomes]
rs10931285	0.92[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1098424	0.85[EUR][1000 genomes]
rs1098425	0.86[EUR][1000 genomes]
rs11883913	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12469000	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475425	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12477273	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12479177	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12619637	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12621307	0.96[CEU][hapmap]
rs12986579	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13018456	0.86[EUR][1000 genomes]
rs13383378	0.87[EUR][1000 genomes]
rs13387337	0.87[EUR][1000 genomes]
rs13406361	0.84[EUR][1000 genomes]
rs13414232	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431546	0.86[EUR][1000 genomes]
rs13432218	0.86[EUR][1000 genomes]
rs13432996	0.85[EUR][1000 genomes]
rs1398060	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511879	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1528235	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1918900	0.86[EUR][1000 genomes]
rs1918906	0.87[EUR][1000 genomes]
rs2882203	0.88[CEU][hapmap]
rs3771076	0.89[CEU][hapmap]
rs3771081	0.96[CEU][hapmap]
rs3771084	0.96[CEU][hapmap]
rs3771089	0.92[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3771091	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4356630	0.85[EUR][1000 genomes]
rs4399679	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4436927	0.86[EUR][1000 genomes]
rs4441433	0.85[EUR][1000 genomes]
rs62172531	0.86[EUR][1000 genomes]
rs6710629	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6742071	0.87[EUR][1000 genomes]
rs6759535	0.92[CEU][hapmap]
rs7597989	0.92[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs870509	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870882	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9646807	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1003061	chr2:187950057-188282330	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000617	chr2:187950057-188290511	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875555	chr2:188023107-188143677	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2751839	chr2:188035947-188141690	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2763652	chr2:188042583-188153257	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1004711	chr2:188044247-188142073	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv997699	chr2:188052351-188142073	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv584032	chr2:188083217-188150228	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv875556	chr2:188083300-188135654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv533935	chr2:188089148-188284766	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv584033	chr2:188103476-188135654	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv584034	chr2:188103476-188143677	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv584035	chr2:188105078-188153421	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1002116	chr2:188119621-188142073	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv431868	chr2:188119621-188159750	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188127400-188129800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:188127400-188129800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr2:188127600-188130600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:188128400-188130000	Flanking Active TSS	HUVEC	blood vessel
5	chr2:188128600-188129800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr2:188128600-188129800	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:188128600-188129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:188128800-188129800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:188129000-188129800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:188129000-188129800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:188129200-188129800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:188129200-188129800	Enhancers	Fetal Lung	lung
13	chr2:188129200-188130200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:188129200-188130400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:188129400-188129800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr2:188129400-188130200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:188129600-188130600	Enhancers	HUES48 Cell Line	embryonic stem cell

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