Variant report

Variant	rs6138435
Chromosome Location	chr20:24945581-24945582
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24944898..24946529-chr20:24971755..24973854,2	MCF-7	breast:
2	chr20:24940462..24942946-chr20:24945395..24947544,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1056033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056036	0.98[ASN][1000 genomes]
rs11087486	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11699285	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11700073	0.88[ASN][1000 genomes]
rs11905625	0.88[ASN][1000 genomes]
rs11906373	0.93[ASN][1000 genomes]
rs12625319	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13041643	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331286	0.81[ASN][1000 genomes]
rs1535042	0.86[ASN][1000 genomes]
rs1854849	0.81[ASN][1000 genomes]
rs1977540	0.84[ASN][1000 genomes]
rs2008275	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2092565	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103736	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151462	0.93[ASN][1000 genomes]
rs2151463	0.93[ASN][1000 genomes]
rs2179729	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179730	0.98[ASN][1000 genomes]
rs2206891	0.91[ASN][1000 genomes]
rs2225459	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235847	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227590	0.84[ASN][1000 genomes]
rs227597	0.81[ASN][1000 genomes]
rs227613	0.88[ASN][1000 genomes]
rs227614	0.91[ASN][1000 genomes]
rs227615	0.86[ASN][1000 genomes]
rs227616	0.93[ASN][1000 genomes]
rs227618	0.86[ASN][1000 genomes]
rs227619	0.91[ASN][1000 genomes]
rs227620	0.91[ASN][1000 genomes]
rs227621	0.93[ASN][1000 genomes]
rs227622	0.93[ASN][1000 genomes]
rs227623	0.91[ASN][1000 genomes]
rs227624	0.93[ASN][1000 genomes]
rs227625	0.93[ASN][1000 genomes]
rs227626	0.91[ASN][1000 genomes]
rs227627	0.91[ASN][1000 genomes]
rs227628	0.91[ASN][1000 genomes]
rs227629	0.93[ASN][1000 genomes]
rs227630	0.93[ASN][1000 genomes]
rs227631	0.93[ASN][1000 genomes]
rs227632	0.93[ASN][1000 genomes]
rs227633	0.91[ASN][1000 genomes]
rs227634	0.91[ASN][1000 genomes]
rs227635	0.91[ASN][1000 genomes]
rs227639	0.91[ASN][1000 genomes]
rs227643	0.91[ASN][1000 genomes]
rs227646	0.91[ASN][1000 genomes]
rs227648	0.91[ASN][1000 genomes]
rs227649	0.81[ASN][1000 genomes]
rs227650	0.91[ASN][1000 genomes]
rs227651	0.93[ASN][1000 genomes]
rs227652	0.91[ASN][1000 genomes]
rs227653	0.91[ASN][1000 genomes]
rs227657	0.91[ASN][1000 genomes]
rs227658	0.93[ASN][1000 genomes]
rs227659	0.91[ASN][1000 genomes]
rs2387365	0.81[ASN][1000 genomes]
rs2387366	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387572	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424691	0.93[ASN][1000 genomes]
rs2892279	0.98[ASN][1000 genomes]
rs34419834	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273288	0.84[ASN][1000 genomes]
rs4527284	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4539860	0.86[ASN][1000 genomes]
rs45468392	0.91[ASN][1000 genomes]
rs45556041	0.91[ASN][1000 genomes]
rs4594518	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813541	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813542	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815327	0.84[ASN][1000 genomes]
rs4815337	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815339	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815340	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815341	0.98[ASN][1000 genomes]
rs4815351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815355	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815357	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56312312	0.88[ASN][1000 genomes]
rs57265446	0.84[ASN][1000 genomes]
rs58244398	0.86[ASN][1000 genomes]
rs6036976	0.84[ASN][1000 genomes]
rs6050134	0.82[ASN][1000 genomes]
rs6050177	0.98[ASN][1000 genomes]
rs6050179	0.98[ASN][1000 genomes]
rs6050181	0.98[ASN][1000 genomes]
rs6050198	0.84[ASN][1000 genomes]
rs6050201	0.98[ASN][1000 genomes]
rs6083684	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083685	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083686	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083688	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083692	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083699	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083709	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6106975	0.98[ASN][1000 genomes]
rs6106984	0.88[ASN][1000 genomes]
rs6114980	0.88[ASN][1000 genomes]
rs6114981	0.88[ASN][1000 genomes]
rs6114984	0.88[ASN][1000 genomes]
rs6114988	0.88[ASN][1000 genomes]
rs6114992	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132773	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132774	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132775	0.91[ASN][1000 genomes]
rs6132777	0.91[ASN][1000 genomes]
rs6132778	0.91[ASN][1000 genomes]
rs6138406	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6138417	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138423	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138425	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138426	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138427	0.85[EUR][1000 genomes]
rs6138431	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138438	0.91[ASN][1000 genomes]
rs6138442	0.86[ASN][1000 genomes]
rs6138453	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138455	0.86[ASN][1000 genomes]
rs6138456	0.86[ASN][1000 genomes]
rs6138457	0.86[ASN][1000 genomes]
rs6138458	0.88[ASN][1000 genomes]
rs6138461	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62215110	0.91[ASN][1000 genomes]
rs62215115	0.91[ASN][1000 genomes]
rs62215128	0.86[ASN][1000 genomes]
rs62215131	0.86[ASN][1000 genomes]
rs6707	0.91[ASN][1000 genomes]
rs7268095	0.88[ASN][1000 genomes]
rs7269416	0.88[ASN][1000 genomes]
rs735886	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8125909	0.86[ASN][1000 genomes]
rs8183891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs914314	0.81[ASN][1000 genomes]
rs926661	0.98[ASN][1000 genomes]
rs926662	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers 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	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138435	APMAP	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24935000-24953600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr20:24935200-24957600	Strong transcription	Liver	Liver
3	chr20:24935200-24971800	Weak transcription	K562	blood
4	chr20:24936000-24955600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:24936200-24947400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr20:24936200-24954400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:24936400-24947000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:24936400-24954400	Strong transcription	Fetal Intestine Small	intestine
9	chr20:24936400-24954400	Strong transcription	Fetal Stomach	stomach
10	chr20:24936400-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:24936400-24954600	Strong transcription	Brain Germinal Matrix	brain
12	chr20:24936400-24954600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr20:24936400-24954800	Strong transcription	Spleen	Spleen
14	chr20:24936400-24956000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:24936600-24945800	Strong transcription	Brain Hippocampus Middle	brain
16	chr20:24936600-24947200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr20:24936600-24950600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr20:24936600-24954200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:24936600-24954200	Strong transcription	Brain Substantia Nigra	brain
20	chr20:24936600-24954200	Strong transcription	Gastric	stomach
21	chr20:24936600-24954800	Strong transcription	Brain Anterior Caudate	brain
22	chr20:24936600-24954800	Strong transcription	Thymus	Thymus
23	chr20:24936800-24952600	Strong transcription	Placenta	Placenta
24	chr20:24936800-24954800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr20:24936800-24955000	Strong transcription	Lung	lung
26	chr20:24936800-24955400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:24936800-24955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:24937000-24950600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr20:24937000-24955000	Strong transcription	Dnd41	blood
30	chr20:24937200-24954400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:24937200-24954400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr20:24937200-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:24937200-24954800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:24937200-24955000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr20:24937400-24954200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:24937400-24957200	Strong transcription	HepG2	liver
37	chr20:24937600-24954600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:24937800-24954400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr20:24937800-24954800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr20:24937800-24955000	Strong transcription	Primary T cells from cord blood	blood
41	chr20:24938000-24948000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr20:24938000-24954600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:24938000-24954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:24938000-24954800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr20:24938200-24954200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr20:24938200-24954200	Strong transcription	Colonic Mucosa	Colon
47	chr20:24938200-24955600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:24938400-24954400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:24938400-24954600	Strong transcription	Fetal Intestine Large	intestine
50	chr20:24938400-24954800	Strong transcription	Fetal Thymus	thymus

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