Variant report

Variant	rs12424348
Chromosome Location	chr12:24989145-24989146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10160847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10466757	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10466800	0.96[ASN][1000 genomes]
rs1054277	0.89[JPT][hapmap]
rs1054279	0.89[JPT][hapmap]
rs10743521	0.80[ASN][1000 genomes]
rs10743522	0.80[ASN][1000 genomes]
rs1075061	0.87[YRI][hapmap];0.92[ASN][1000 genomes]
rs1075063	0.80[ASW][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs10771127	0.89[JPT][hapmap]
rs10771134	0.87[ASN][1000 genomes]
rs10771138	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10842417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10842420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11047684	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11047686	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11047689	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11609552	0.86[JPT][hapmap]
rs11613673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11613710	0.86[ASN][1000 genomes]
rs11615863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12227952	0.96[ASN][1000 genomes]
rs12228257	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12296255	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12301149	0.86[ASN][1000 genomes]
rs12302883	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12319639	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12425320	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1392195	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1392196	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1471844	0.89[JPT][hapmap]
rs16928089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17372766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872644	0.89[JPT][hapmap]
rs1872645	0.89[JPT][hapmap]
rs2046524	0.89[JPT][hapmap]
rs2062497	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2133582	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2133583	0.86[ASN][1000 genomes]
rs2200509	0.89[JPT][hapmap]
rs2220269	0.89[JPT][hapmap]
rs2220271	0.89[ASN][1000 genomes]
rs2353478	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs2353483	0.89[JPT][hapmap]
rs3198082	0.89[JPT][hapmap]
rs3736211	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4522264	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4963805	0.95[ASN][1000 genomes]
rs4963806	0.95[ASN][1000 genomes]
rs4963808	0.93[ASN][1000 genomes]
rs4963814	0.92[ASN][1000 genomes]
rs60104197	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914865	0.93[ASN][1000 genomes]
rs6487419	0.89[JPT][hapmap]
rs6487420	1.00[JPT][hapmap]
rs6487434	0.92[CHB][hapmap]
rs6487437	1.00[CHB][hapmap]
rs7138685	0.97[ASN][1000 genomes]
rs718567	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7296211	0.89[JPT][hapmap]
rs7305794	0.89[JPT][hapmap]
rs73061805	0.82[ASN][1000 genomes]
rs73061812	0.81[ASN][1000 genomes]
rs73079552	0.93[ASN][1000 genomes]
rs73079568	0.84[ASN][1000 genomes]
rs73079570	0.86[ASN][1000 genomes]
rs7308285	0.93[ASN][1000 genomes]
rs7310300	0.89[JPT][hapmap]
rs7961152	0.80[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs7961688	0.91[ASN][1000 genomes]
rs7961778	0.82[ASN][1000 genomes]
rs7962203	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs7966783	0.80[ASN][1000 genomes]
rs7973974	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7976928	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs937503	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs954199	0.84[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs954201	0.83[CHB][hapmap];0.81[JPT][hapmap]

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
rs12424348	REP15	cis	cerebellum	SCAN

Chromatin state (count:66 , 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	chr12:24965200-24989800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:24965600-24989400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:24965600-25004800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:24965800-24989800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:24966200-24989600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:24966200-25002000	Weak transcription	HepG2	liver
8	chr12:24967000-24989600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:24968000-24990800	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:24968000-25017600	Weak transcription	Fetal Thymus	thymus
11	chr12:24968400-25007800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:24969000-24991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:24969200-25002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:24969600-24989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:24971000-25054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:24971400-24995600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:24972000-24990800	Weak transcription	Fetal Stomach	stomach
18	chr12:24972000-25004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:24972400-24990800	Weak transcription	Placenta	Placenta
20	chr12:24973400-24991400	Weak transcription	Fetal Brain Male	brain
21	chr12:24974400-25001800	Weak transcription	Pancreas	Pancrea
22	chr12:24975000-24989200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:24975000-24992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:24975400-24989400	Weak transcription	Ovary	ovary
25	chr12:24975600-24992000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:24975600-24993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:24975800-24990800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:24976400-24993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:24978600-24989800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr12:24979200-25007000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:24981200-24990800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:24982400-24990800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:24983800-24990800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:24985200-24994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:24985800-24990600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:24985800-24990800	Weak transcription	Fetal Lung	lung
37	chr12:24985800-24991400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:24985800-24994800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:24986000-24990600	Weak transcription	HSMMtube	muscle
40	chr12:24986000-24990800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:24986000-24990800	Weak transcription	NHLF	lung
42	chr12:24986200-24989400	Weak transcription	Dnd41	blood
43	chr12:24986200-24990200	Weak transcription	GM12878-XiMat	blood
44	chr12:24986200-24990800	Weak transcription	Osteobl	bone
45	chr12:24986200-24991800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:24986200-24995000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:24986400-24992200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:24986800-24997000	Strong transcription	HUVEC	blood vessel
49	chr12:24987000-24990800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:24987000-24991400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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