Variant report

Variant	rs11580609
Chromosome Location	chr1:45975856-45975857
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45974939..45977846-chr1:46015282..46017928,2	MCF-7	breast:
2	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
3	chr1:45974971..45980027-chr1:46048272..46053531,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1A1-3	chr1:45975647-45976177	NONHSAT002944

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10789465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10890331	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11211109	0.81[ASN][1000 genomes]
rs11211122	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211130	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211135	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211136	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11582118	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12119202	0.80[AMR][1000 genomes]
rs12133294	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12139364	0.95[CHB][hapmap]
rs12568144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729715	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12738318	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12743512	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2275276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2356413	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2356551	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2356553	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2453404	0.80[EUR][1000 genomes]
rs2934856	0.82[EUR][1000 genomes]
rs2934859	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2991970	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2991971	0.81[EUR][1000 genomes]
rs2991972	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2991973	0.81[EUR][1000 genomes]
rs2991974	0.81[EUR][1000 genomes]
rs2993262	0.82[EUR][1000 genomes]
rs35092140	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4660861	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4660869	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660876	0.82[EUR][1000 genomes]
rs512026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518365	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523526	0.82[EUR][1000 genomes]
rs60608374	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606542	0.81[EUR][1000 genomes]
rs622798	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs644915	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6661321	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666720	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs667626	0.82[EUR][1000 genomes]
rs7526571	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526665	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs781058	0.95[CHB][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9147	0.82[EUR][1000 genomes]
rs937291	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9429079	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs945180	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998199	0.91[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS 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 target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS 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 target site	232 gene(s)	inside rSNPs	diseases
9	nsv932954	chr1:45975022-45976755	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11580609	CCDC163P	cis	Artery Aorta	GTEx
rs11580609	CCDC163P	cis	Whole Blood	GTEx
rs11580609	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs11580609	CCDC163P	cis	Stomach	GTEx
rs11580609	CCDC163P	cis	Nerve Tibial	GTEx
rs11580609	GPBP1L1	cis	Whole Blood	GTEx
rs11580609	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs11580609	CCDC163P	cis	Heart Left Ventricle	GTEx
rs11580609	CCDC163P	cis	Muscle Skeletal	GTEx
rs11580609	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs11580609	CCDC163P	cis	Esophagus Muscularis	GTEx
rs11580609	CCDC163P	cis	Artery Tibial	GTEx
rs11580609	CCDC163P	cis	Esophagus Mucosa	GTEx
rs11580609	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs11580609	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs11580609	CCDC163P	cis	Thyroid	GTEx
rs11580609	CCDC163P	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45966600-45984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:45966800-45976000	Weak transcription	Fetal Brain Male	brain
3	chr1:45966800-45976000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:45966800-45980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:45967000-45977200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:45967200-45976200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:45967200-45976200	Weak transcription	Fetal Lung	lung
9	chr1:45971600-45985000	Strong transcription	Fetal Stomach	stomach
10	chr1:45971800-45980400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:45971800-45982000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:45972800-45978200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:45972800-45978400	Strong transcription	Fetal Intestine Small	intestine
14	chr1:45972800-45980400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:45972800-45982200	Strong transcription	K562	blood
16	chr1:45972800-45982400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:45972800-45984400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:45972800-45984400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:45972800-45984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:45972800-45984600	Strong transcription	Fetal Thymus	thymus
21	chr1:45973000-45976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:45973000-45981800	Strong transcription	Dnd41	blood
23	chr1:45973000-45983000	Strong transcription	Fetal Brain Female	brain
24	chr1:45973000-45983200	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr1:45973000-45983200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:45973000-45983400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:45973000-45983800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:45973000-45983800	Strong transcription	Spleen	Spleen
29	chr1:45973000-45984000	Strong transcription	Primary T cells from cord blood	blood
30	chr1:45973000-45984000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:45973000-45984000	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:45973000-45984400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:45973000-45984400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:45973000-45984600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr1:45973200-45976400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:45973200-45978200	Strong transcription	Thymus	Thymus
37	chr1:45973200-45978600	Strong transcription	Fetal Intestine Large	intestine
38	chr1:45973200-45978800	Genic enhancers	Brain Substantia Nigra	brain
39	chr1:45973200-45982000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:45973200-45982200	Strong transcription	NHEK	skin
41	chr1:45973200-45982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:45973200-45983200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:45973200-45983600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:45973200-45983800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:45973200-45984200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:45973200-45984600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:45973200-45984600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:45973200-45984600	Strong transcription	Adipose Nuclei	Adipose
49	chr1:45973400-45978800	Strong transcription	Hela-S3	cervix
50	chr1:45973400-45979800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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