Variant report

Variant	rs6671239
Chromosome Location	chr1:46130113-46130114
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46126286..46130719-chr1:46131581..46134748,5	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1053941	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11579176	0.83[AMR][1000 genomes]
rs11585275	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11587918	0.89[EUR][1000 genomes]
rs11587982	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11590549	0.84[EUR][1000 genomes]
rs28412451	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28433203	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28484896	0.89[EUR][1000 genomes]
rs28584711	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3014232	0.94[EUR][1000 genomes]
rs41310432	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55659201	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55951835	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56020747	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56093189	0.85[EUR][1000 genomes]
rs56238114	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56251392	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58692133	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61056720	0.80[EUR][1000 genomes]
rs6429573	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6662572	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6662999	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72688452	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72688460	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517111	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7541935	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9429173	0.85[AMR][1000 genomes];0.89[EUR][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	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
2	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
3	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
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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 lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6671239	CCDC163P	cis	Nerve Tibial	GTEx
rs6671239	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs6671239	CCDC163P	cis	Artery Aorta	GTEx
rs6671239	CCDC163P	cis	Heart Left Ventricle	GTEx
rs6671239	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs6671239	CCDC163P	cis	Esophagus Mucosa	GTEx
rs6671239	CCDC163P	cis	Artery Tibial	GTEx
rs6671239	CCDC163P	cis	Stomach	GTEx
rs6671239	CCDC163P	cis	Whole Blood	GTEx
rs6671239	CCDC163P	cis	Thyroid	GTEx
rs6671239	TMEM69	Cis_1M	lymphoblastoid	RTeQTL
rs6671239	CCDC163P	cis	Muscle Skeletal	GTEx
rs6671239	CCDC163P	cis	Esophagus Muscularis	GTEx
rs6671239	CCDC163P	cis	lung	GTEx
rs6671239	CCDC163P	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46098400-46133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46100200-46135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:46106200-46140000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:46113800-46133400	Weak transcription	Right Atrium	heart
5	chr1:46121000-46135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:46123400-46134000	Weak transcription	Gastric	stomach
7	chr1:46124400-46135000	Weak transcription	A549	lung
8	chr1:46124800-46132400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:46124800-46144600	Weak transcription	Aorta	Aorta
10	chr1:46125000-46148400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:46125200-46133200	Weak transcription	Stomach Mucosa	stomach
12	chr1:46125200-46135000	Weak transcription	NH-A	brain
13	chr1:46125200-46151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:46125400-46135800	Weak transcription	Fetal Brain Male	brain
15	chr1:46125400-46140000	Weak transcription	NHEK	skin
16	chr1:46125600-46134800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:46125800-46132400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:46126000-46132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:46126000-46132200	Weak transcription	HSMMtube	muscle
20	chr1:46126000-46132400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:46126000-46133000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:46126000-46133200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:46126000-46133200	Weak transcription	Spleen	Spleen
24	chr1:46126000-46133400	Weak transcription	Lung	lung
25	chr1:46126000-46133400	Weak transcription	Pancreas	Pancrea
26	chr1:46126000-46134800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:46126000-46135000	Weak transcription	Right Ventricle	heart
28	chr1:46126000-46137000	Weak transcription	Esophagus	oesophagus
29	chr1:46126000-46143000	Weak transcription	Fetal Lung	lung
30	chr1:46126000-46143800	Weak transcription	Fetal Brain Female	brain
31	chr1:46126000-46144200	Weak transcription	Brain Germinal Matrix	brain
32	chr1:46126000-46145000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:46126000-46147200	Weak transcription	Thymus	Thymus
34	chr1:46126000-46149000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:46126000-46151000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:46126200-46132600	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:46126200-46132600	Weak transcription	Ovary	ovary
38	chr1:46126200-46132800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:46126200-46133600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:46126200-46134400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:46126200-46138400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:46126200-46138800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:46126200-46140000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:46126200-46140200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:46126200-46144800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:46126200-46148600	Weak transcription	Fetal Stomach	stomach
47	chr1:46126400-46133200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:46126400-46134400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:46126400-46134400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:46126400-46134400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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