Variant report

Variant	rs2200509
Chromosome Location	chr12:24970588-24970589
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10128933	1.00[ASN][1000 genomes]
rs10160847	0.90[JPT][hapmap]
rs1054277	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1054279	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1054281	1.00[ASN][1000 genomes]
rs10743521	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743522	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1075063	1.00[JPT][hapmap]
rs10771127	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10771128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842417	0.90[JPT][hapmap]
rs10842420	0.89[JPT][hapmap]
rs11047684	0.93[CEU][hapmap]
rs11047686	0.93[CEU][hapmap]
rs11047689	0.87[CEU][hapmap]
rs11047696	0.89[JPT][hapmap]
rs11609552	0.88[JPT][hapmap]
rs11613673	0.89[JPT][hapmap]
rs11615863	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12296255	0.93[CEU][hapmap]
rs12302883	0.93[CEU][hapmap]
rs12319639	0.93[CEU][hapmap]
rs12424348	0.89[JPT][hapmap]
rs12425320	0.93[CEU][hapmap]
rs1392195	0.93[CEU][hapmap]
rs1471842	1.00[ASN][1000 genomes]
rs1471843	1.00[ASN][1000 genomes]
rs1471844	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16928089	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs16928173	0.89[JPT][hapmap]
rs1872644	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1872645	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2046524	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2062497	0.93[CEU][hapmap]
rs2133582	0.93[CEU][hapmap]
rs2220269	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2220270	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353478	0.89[JPT][hapmap]
rs2353481	1.00[ASN][1000 genomes]
rs2353482	1.00[ASN][1000 genomes]
rs2353483	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3198082	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3736211	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs3926539	1.00[ASN][1000 genomes]
rs4143212	0.89[JPT][hapmap]
rs4400889	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4453321	1.00[ASN][1000 genomes]
rs4963802	0.80[EUR][1000 genomes]
rs6487419	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6487420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs6487421	1.00[ASN][1000 genomes]
rs7134619	1.00[ASN][1000 genomes]
rs7134734	1.00[ASN][1000 genomes]
rs7134871	0.97[ASN][1000 genomes]
rs718567	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7296211	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7296995	1.00[ASN][1000 genomes]
rs7305794	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7310300	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7962203	0.89[JPT][hapmap]
rs7966783	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7976928	0.89[JPT][hapmap]
rs7977807	0.87[CEU][hapmap]
rs937503	0.93[CEU][hapmap]
rs954199	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs9988971	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9989035	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
6	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
7	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
10	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1045302	chr12:24921100-25078227	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
17	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1054863	chr12:24941350-25078227	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
20	nsv541426	chr12:24941350-25078227	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
21	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
24	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
25	nsv557794	chr12:24964383-24970708	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2200509	BCAT1	Cis_1M	lymphoblastoid	RTeQTL
rs2200509	BCAT1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24960400-24975200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:24964000-25013400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:24964400-24973600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:24965200-24976800	Weak transcription	Lung	lung
5	chr12:24965200-24989800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:24965600-24986800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:24965600-24989400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:24965600-25004800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:24965800-24971000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:24965800-24974200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:24965800-24989800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:24966200-24973600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:24966200-24974800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:24966200-24987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:24966200-24989600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:24966200-25002000	Weak transcription	HepG2	liver
17	chr12:24967000-24989600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:24967400-24974800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:24967600-24971000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:24967600-24971200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:24967600-24977800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr12:24967800-24970800	Strong transcription	Osteobl	bone
23	chr12:24967800-24989000	Weak transcription	Aorta	Aorta
24	chr12:24968000-24973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:24968000-24974000	Weak transcription	NHEK	skin
26	chr12:24968000-24974200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:24968000-24976400	Strong transcription	K562	blood
28	chr12:24968000-24990800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:24968000-25017600	Weak transcription	Fetal Thymus	thymus
30	chr12:24968200-24972200	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr12:24968200-24973400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:24968200-24973600	Weak transcription	Ovary	ovary
33	chr12:24968200-24985000	Weak transcription	Fetal Lung	lung
34	chr12:24968200-24986800	Weak transcription	Thymus	Thymus
35	chr12:24968400-24972800	Strong transcription	NH-A	brain
36	chr12:24968400-24983600	Weak transcription	Fetal Kidney	kidney
37	chr12:24968400-25007800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:24968600-24974800	Weak transcription	Small Intestine	intestine
39	chr12:24968600-24980600	Weak transcription	Fetal Brain Female	brain
40	chr12:24968800-24971000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr12:24968800-24972600	Weak transcription	GM12878-XiMat	blood
42	chr12:24968800-24974000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:24969000-24976200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:24969000-24991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:24969200-25002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:24969400-24971000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:24969400-24981600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:24969600-24970600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:24969600-24973800	Strong transcription	HSMM	muscle
50	chr12:24969600-24981600	Strong transcription	Dnd41	blood

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