Variant report

Variant	rs12317452
Chromosome Location	chr12:123788246-123788247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 186 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs10082867	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444439	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10444449	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744151	0.82[JPT][hapmap]
rs10744152	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10744153	0.81[ASN][1000 genomes]
rs10744154	0.81[ASN][1000 genomes]
rs10772997	0.85[JPT][hapmap]
rs10773000	0.94[JPT][hapmap]
rs10773003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773007	1.00[YRI][hapmap]
rs10773014	1.00[YRI][hapmap]
rs10773018	0.80[ASN][1000 genomes]
rs10846489	0.94[JPT][hapmap]
rs10846497	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846505	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10846509	1.00[YRI][hapmap]
rs10846510	1.00[YRI][hapmap]
rs10846514	1.00[YRI][hapmap]
rs10846517	0.82[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10846518	1.00[YRI][hapmap]
rs10846519	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10846523	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11057223	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11057238	0.88[ASN][1000 genomes]
rs11057240	1.00[YRI][hapmap]
rs11057242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057248	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057250	1.00[YRI][hapmap]
rs11057251	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11057254	0.98[ASN][1000 genomes]
rs11057261	0.98[ASN][1000 genomes]
rs11057266	1.00[YRI][hapmap]
rs11057273	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057275	0.95[ASN][1000 genomes]
rs11057276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11057283	0.81[ASN][1000 genomes]
rs11057284	0.98[ASN][1000 genomes]
rs11057287	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1109559	0.94[JPT][hapmap]
rs1109560	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs11503021	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11608297	0.87[ASN][1000 genomes]
rs11608305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11611141	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611677	0.96[ASN][1000 genomes]
rs11611679	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11611680	0.94[ASN][1000 genomes]
rs11611694	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612234	0.81[ASN][1000 genomes]
rs12317103	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12366872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12367421	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12371973	1.00[YRI][hapmap]
rs12582153	0.98[ASN][1000 genomes]
rs13303208	0.91[ASN][1000 genomes]
rs1402275	0.85[YRI][hapmap]
rs1568428	0.94[JPT][hapmap]
rs1615350	0.84[JPT][hapmap]
rs1727293	0.90[JPT][hapmap]
rs1727295	0.85[JPT][hapmap]
rs1727301	0.85[JPT][hapmap]
rs1727302	0.84[JPT][hapmap]
rs1790104	0.86[JPT][hapmap]
rs1790106	0.80[JPT][hapmap]
rs1790121	0.80[JPT][hapmap]
rs1879379	0.94[JPT][hapmap]
rs2271976	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2682427	0.85[JPT][hapmap]
rs28410096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28414347	0.84[JPT][hapmap]
rs28418709	0.81[ASN][1000 genomes]
rs28419092	0.98[ASN][1000 genomes]
rs28450974	0.97[ASN][1000 genomes]
rs28461471	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28475177	1.00[YRI][hapmap]
rs28496545	0.90[ASN][1000 genomes]
rs28498205	0.97[ASN][1000 genomes]
rs28501453	0.84[JPT][hapmap]
rs28503862	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28516750	0.93[ASN][1000 genomes]
rs28517382	0.81[ASN][1000 genomes]
rs28532037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28533432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28556815	0.86[ASN][1000 genomes]
rs28565984	0.83[ASN][1000 genomes]
rs28574664	0.81[ASN][1000 genomes]
rs28577594	0.91[ASN][1000 genomes]
rs28581850	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28587386	0.84[JPT][hapmap]
rs28592032	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28594416	0.81[ASN][1000 genomes]
rs28595660	0.84[JPT][hapmap]
rs28613486	0.84[JPT][hapmap]
rs28631104	0.91[ASN][1000 genomes]
rs28631903	0.81[ASN][1000 genomes]
rs28642812	0.91[ASN][1000 genomes]
rs28655516	1.00[YRI][hapmap]
rs28660993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28690326	0.85[ASN][1000 genomes]
rs28703745	0.80[ASN][1000 genomes]
rs28718696	0.80[ASN][1000 genomes]
rs28759130	0.81[ASN][1000 genomes]
rs28786830	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28820735	0.97[ASN][1000 genomes]
rs28825193	0.97[ASN][1000 genomes]
rs28866344	0.93[ASN][1000 genomes]
rs3088303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34032470	0.87[ASN][1000 genomes]
rs35818434	0.97[ASN][1000 genomes]
rs3803001	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3825141	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4759374	0.83[ASN][1000 genomes]
rs4759375	1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4759376	0.81[ASN][1000 genomes]
rs4759377	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759421	0.81[ASN][1000 genomes]
rs56116847	0.98[ASN][1000 genomes]
rs56197170	0.85[ASN][1000 genomes]
rs56309603	0.89[ASN][1000 genomes]
rs57356592	0.83[ASN][1000 genomes]
rs57416942	0.81[ASN][1000 genomes]
rs58537268	0.83[ASN][1000 genomes]
rs58948739	0.83[ASN][1000 genomes]
rs59295450	0.81[ASN][1000 genomes]
rs60755632	0.83[ASN][1000 genomes]
rs60835840	0.95[ASN][1000 genomes]
rs61058270	0.83[ASN][1000 genomes]
rs61388686	0.98[ASN][1000 genomes]
rs61751327	0.81[ASN][1000 genomes]
rs61953412	0.81[ASN][1000 genomes]
rs61955125	0.89[ASN][1000 genomes]
rs6416290	0.85[ASN][1000 genomes]
rs6488869	0.81[ASN][1000 genomes]
rs6488870	0.81[ASN][1000 genomes]
rs6488871	0.81[ASN][1000 genomes]
rs6488872	0.81[ASN][1000 genomes]
rs6488873	0.89[ASN][1000 genomes]
rs7137243	0.81[ASN][1000 genomes]
rs7139321	0.95[JPT][hapmap]
rs7297649	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7298909	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7301163	0.81[ASN][1000 genomes]
rs7303754	0.85[ASN][1000 genomes]
rs7310756	0.81[ASN][1000 genomes]
rs7311304	0.81[ASN][1000 genomes]
rs7312145	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73216931	0.92[ASN][1000 genomes]
rs73231950	0.98[ASN][1000 genomes]
rs7484644	0.81[ASN][1000 genomes]
rs7485967	0.81[ASN][1000 genomes]
rs7486223	0.81[ASN][1000 genomes]
rs7488340	0.81[ASN][1000 genomes]
rs7488490	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952835	0.81[ASN][1000 genomes]
rs7954704	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955367	0.81[ASN][1000 genomes]
rs7959415	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7970080	0.81[ASN][1000 genomes]
rs7972811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973131	0.81[ASN][1000 genomes]
rs7973878	0.81[ASN][1000 genomes]
rs7974099	0.88[ASN][1000 genomes]
rs7977563	0.81[ASN][1000 genomes]
rs9284166	0.81[ASN][1000 genomes]
rs9300257	0.81[ASN][1000 genomes]
rs9300259	0.80[ASN][1000 genomes]
rs949143	0.80[JPT][hapmap]
rs9669169	0.81[ASN][1000 genomes]
rs9669273	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9669295	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9705407	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9739171	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9739565	0.81[ASN][1000 genomes]
rs9795593	0.83[JPT][hapmap];0.81[ASN][1000 genomes]

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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12317452	CDK2AP1	cis	Whole Blood	GTEx
rs12317452	RP11-282O18.3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123771600-123799800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123771800-123790800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:123772400-123799800	Strong transcription	Fetal Stomach	stomach
4	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:123772800-123789400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:123772800-123821000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:123773000-123835200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:123773200-123830600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:123773200-123834200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:123773200-123835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:123773200-123835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:123773400-123797800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:123773400-123811600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:123773400-123812400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:123773400-123826200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:123773400-123826200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:123773400-123826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:123773400-123835000	Strong transcription	Fetal Thymus	thymus
20	chr12:123773400-123835400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:123773600-123789200	Strong transcription	Brain Germinal Matrix	brain
23	chr12:123773600-123816000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:123773600-123830800	Strong transcription	Placenta	Placenta
25	chr12:123773600-123835200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:123773600-123835400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:123773800-123798200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:123773800-123798400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:123773800-123826200	Strong transcription	Adipose Nuclei	Adipose
30	chr12:123773800-123826200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr12:123773800-123834800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:123774000-123788600	Weak transcription	Stomach Mucosa	stomach
35	chr12:123774000-123789600	Strong transcription	Fetal Intestine Large	intestine
36	chr12:123774000-123798600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:123774000-123802800	Strong transcription	Osteobl	bone
38	chr12:123774000-123820600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:123774000-123821600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:123774000-123835000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr12:123774000-123835200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:123774000-123835400	Strong transcription	Dnd41	blood
43	chr12:123774400-123821200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:123774600-123788600	Strong transcription	NHEK	skin
45	chr12:123774600-123822200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:123775000-123797200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:123775400-123798600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:123775600-123812200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:123775600-123835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:123775800-123821000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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