Variant report

Variant	rs9988971
Chromosome Location	chr12:24976409-24976410
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10128933	0.88[ASN][1000 genomes]
rs10466800	0.80[ASN][1000 genomes]
rs1054277	0.85[ASN][1000 genomes]
rs1054279	0.88[ASN][1000 genomes]
rs1054281	0.88[ASN][1000 genomes]
rs10743521	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743522	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1075061	0.84[ASN][1000 genomes]
rs1075063	0.84[ASN][1000 genomes]
rs10771127	0.88[ASN][1000 genomes]
rs10771128	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12227952	0.80[ASN][1000 genomes]
rs1471842	0.88[ASN][1000 genomes]
rs1471843	0.88[ASN][1000 genomes]
rs1471844	0.88[ASN][1000 genomes]
rs16928089	0.80[ASN][1000 genomes]
rs1872644	0.84[ASN][1000 genomes]
rs1872645	0.88[ASN][1000 genomes]
rs2046524	0.88[ASN][1000 genomes]
rs2200509	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2220269	0.88[ASN][1000 genomes]
rs2220270	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2353481	0.88[ASN][1000 genomes]
rs2353482	0.88[ASN][1000 genomes]
rs2353483	0.88[ASN][1000 genomes]
rs3198082	0.88[ASN][1000 genomes]
rs3736211	0.80[ASN][1000 genomes]
rs3926539	0.88[ASN][1000 genomes]
rs4400889	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453321	0.88[ASN][1000 genomes]
rs4963802	0.80[EUR][1000 genomes]
rs4963805	0.81[ASN][1000 genomes]
rs4963806	0.81[ASN][1000 genomes]
rs4963808	0.83[ASN][1000 genomes]
rs6487419	0.88[ASN][1000 genomes]
rs6487420	0.88[ASN][1000 genomes]
rs6487421	0.88[ASN][1000 genomes]
rs7134619	0.88[ASN][1000 genomes]
rs7134734	0.88[ASN][1000 genomes]
rs7134871	0.85[ASN][1000 genomes]
rs718567	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7296211	0.88[ASN][1000 genomes]
rs7296995	0.88[ASN][1000 genomes]
rs7305794	0.88[ASN][1000 genomes]
rs7310300	0.88[ASN][1000 genomes]
rs7956863	0.83[ASN][1000 genomes]
rs7961152	0.81[ASN][1000 genomes]
rs7966783	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970244	0.83[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	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9988971	BCAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24964000-25013400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:24965200-24976800	Weak transcription	Lung	lung
3	chr12:24965200-24989800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:24965600-24986800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:24965600-24989400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:24965600-25004800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:24965800-24989800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:24966200-24987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:24966200-24989600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:24966200-25002000	Weak transcription	HepG2	liver
11	chr12:24967000-24989600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:24967600-24977800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr12:24967800-24989000	Weak transcription	Aorta	Aorta
14	chr12:24968000-24990800	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:24968000-25017600	Weak transcription	Fetal Thymus	thymus
16	chr12:24968200-24985000	Weak transcription	Fetal Lung	lung
17	chr12:24968200-24986800	Weak transcription	Thymus	Thymus
18	chr12:24968400-24983600	Weak transcription	Fetal Kidney	kidney
19	chr12:24968400-25007800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:24968600-24980600	Weak transcription	Fetal Brain Female	brain
21	chr12:24969000-24991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:24969200-25002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:24969400-24981600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:24969600-24981600	Strong transcription	Dnd41	blood
25	chr12:24969600-24989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:24970000-24986400	Strong transcription	HUVEC	blood vessel
27	chr12:24970400-24985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:24971000-25054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:24971400-24995600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:24972000-24990800	Weak transcription	Fetal Stomach	stomach
31	chr12:24972000-25004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:24972400-24990800	Weak transcription	Placenta	Placenta
33	chr12:24972800-24987000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:24973400-24991400	Weak transcription	Fetal Brain Male	brain
35	chr12:24974400-24976600	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:24974400-25001800	Weak transcription	Pancreas	Pancrea
37	chr12:24975000-24978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:24975000-24989200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:24975000-24992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:24975200-24977000	Enhancers	Primary B cells from peripheral blood	blood
41	chr12:24975200-24977200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:24975200-24980000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:24975400-24978800	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:24975400-24989400	Weak transcription	Ovary	ovary
45	chr12:24975600-24983200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:24975600-24984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:24975600-24992000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:24975600-24993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:24975800-24976800	Weak transcription	NH-A	brain
50	chr12:24975800-24978800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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