Variant report

Variant	rs12749658
Chromosome Location	chr1:45983348-45983349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
2	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
3	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
4	chr1:45982200..45984064-chr1:46014948..46017218,2	MCF-7	breast:
5	chr1:45974188..45977589-chr1:45979134..45984422,9	MCF-7	breast:
6	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
7	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
8	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
9	chr1:45478829..45481780-chr1:45982107..45984522,2	K562	blood:
10	chr1:45982314..45985214-chr1:46047500..46050905,5	MCF-7	breast:
11	chr1:45978447..45985278-chr1:46015169..46019739,8	MCF-7	breast:
12	chr1:45980815..45983506-chr1:46002846..46004732,2	MCF-7	breast:
13	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000132763	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10157597	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1044717	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10736426	0.93[EUR][1000 genomes]
rs10789466	0.94[EUR][1000 genomes]
rs1088099	0.91[EUR][1000 genomes]
rs11211132	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211134	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12038608	0.88[EUR][1000 genomes]
rs12048936	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12082256	0.85[EUR][1000 genomes]
rs12145526	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12729974	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1337902	0.91[EUR][1000 genomes]
rs1494813	0.91[EUR][1000 genomes]
rs1974271	0.92[EUR][1000 genomes]
rs2077808	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2152077	0.93[EUR][1000 genomes]
rs2356555	0.91[EUR][1000 genomes]
rs2356560	0.93[EUR][1000 genomes]
rs2356561	0.93[EUR][1000 genomes]
rs2991966	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2993257	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2993259	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34315657	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3748643	0.91[EUR][1000 genomes]
rs4233498	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660306	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660309	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660860	0.91[EUR][1000 genomes]
rs4660862	0.91[EUR][1000 genomes]
rs4660864	0.91[EUR][1000 genomes]
rs4660867	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4660868	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660871	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660872	0.91[EUR][1000 genomes]
rs6429567	0.91[EUR][1000 genomes]
rs6429569	0.91[EUR][1000 genomes]
rs6664869	0.83[AMR][1000 genomes]
rs6667191	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6688424	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6688516	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7516006	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7522705	0.92[EUR][1000 genomes]
rs7534467	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7536557	0.92[EUR][1000 genomes]
rs7539253	0.87[EUR][1000 genomes]
rs7543076	0.91[EUR][1000 genomes]
rs7546268	0.91[EUR][1000 genomes]
rs7549093	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs781066	0.91[EUR][1000 genomes]
rs882803	0.93[EUR][1000 genomes]
rs937290	0.91[EUR][1000 genomes]
rs945179	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9725380	0.89[EUR][1000 genomes]
rs9803979	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12749658	CCDC163P	cis	lung	GTEx
rs12749658	CCDC163P	cis	Artery Aorta	GTEx
rs12749658	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs12749658	CCDC163P	cis	Artery Tibial	GTEx
rs12749658	CCDC163P	cis	Thyroid	GTEx
rs12749658	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12749658	CCDC163P	cis	Stomach	GTEx
rs12749658	CCDC163P	cis	Nerve Tibial	GTEx
rs12749658	CCDC163P	cis	Whole Blood	GTEx
rs12749658	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12749658	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12749658	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12749658	CCDC163P	cis	Muscle Skeletal	GTEx
rs12749658	CCDC163P	cis	Heart Left Ventricle	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	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:45971600-45985000	Strong transcription	Fetal Stomach	stomach
4	chr1:45972800-45984400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:45972800-45984400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:45972800-45984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:45972800-45984600	Strong transcription	Fetal Thymus	thymus
8	chr1:45973000-45983400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr1:45973000-45983800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:45973000-45983800	Strong transcription	Spleen	Spleen
11	chr1:45973000-45984000	Strong transcription	Primary T cells from cord blood	blood
12	chr1:45973000-45984000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:45973000-45984000	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:45973000-45984400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:45973000-45984400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:45973000-45984600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:45973200-45983600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:45973200-45983800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:45973200-45984200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:45973200-45984600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:45973200-45984600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:45973200-45984600	Strong transcription	Adipose Nuclei	Adipose
23	chr1:45973400-45983800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:45973400-45984200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:45973400-45984400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:45973400-45984600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:45973600-45984200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:45973800-45984800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:45974000-45983800	Strong transcription	HUVEC	blood vessel
30	chr1:45974200-45984600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:45974400-45984400	Strong transcription	Osteobl	bone
32	chr1:45974800-45984000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:45975400-45983800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:45975400-45984400	Strong transcription	NH-A	brain
35	chr1:45975400-45984800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:45975600-45983800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr1:45975600-45984400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:45975600-45984400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:45976200-45983600	Strong transcription	Fetal Lung	lung
40	chr1:45977000-45984200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:45978200-45983800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:45978400-45983600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:45978400-45983600	Genic enhancers	Placenta	Placenta
44	chr1:45978600-45983800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:45978600-45985000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:45978800-45983800	Strong transcription	Brain Hippocampus Middle	brain
47	chr1:45978800-45984000	Strong transcription	Brain Anterior Caudate	brain
48	chr1:45979000-45983600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:45979000-45984800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:45979200-45984000	Strong transcription	Thymus	Thymus

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