Variant report

Variant	rs56067046
Chromosome Location	chr1:46044314-46044315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45812595..45814836-chr1:46042720..46044656,2	K562	blood:
2	chr1:46043649..46047416-chr1:46047488..46051012,9	K562	blood:
3	chr1:46044070..46047020-chr1:46047607..46050763,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1053941	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11579176	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585275	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3014232	1.00[ASN][1000 genomes]
rs41310432	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[ASN][1000 genomes]
rs55951835	1.00[ASN][1000 genomes]
rs56020747	1.00[ASN][1000 genomes]
rs56238114	1.00[ASN][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs58692133	1.00[ASN][1000 genomes]
rs6429573	1.00[ASN][1000 genomes]
rs6662999	1.00[ASN][1000 genomes]
rs72688452	1.00[ASN][1000 genomes]
rs72688460	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7517111	1.00[ASN][1000 genomes]
rs7553374	1.00[ASN][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	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
3	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
4	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
5	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
6	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
7	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
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs56067046	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs56067046	CCDC163P	cis	Muscle Skeletal	GTEx
rs56067046	CCDC163P	cis	Whole Blood	GTEx
rs56067046	CCDC163P	cis	Esophagus Muscularis	GTEx
rs56067046	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs56067046	CCDC163P	cis	Artery Tibial	GTEx
rs56067046	CCDC163P	cis	Artery Aorta	GTEx
rs56067046	CCDC163P	cis	Stomach	GTEx
rs56067046	CCDC163P	cis	lung	GTEx
rs56067046	CCDC163P	cis	Nerve Tibial	GTEx
rs56067046	CCDC163P	cis	Esophagus Mucosa	GTEx
rs56067046	CCDC163P	cis	Heart Left Ventricle	GTEx
rs56067046	CCDC163P	cis	Thyroid	GTEx
rs56067046	CCDC163P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46032600-46049000	Weak transcription	Right Atrium	heart
2	chr1:46033000-46048800	Weak transcription	Fetal Brain Male	brain
3	chr1:46034200-46048800	Weak transcription	Stomach Mucosa	stomach
4	chr1:46035400-46048800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:46035600-46048000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:46035600-46048800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:46035800-46048800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:46035800-46048800	Weak transcription	Hela-S3	cervix
9	chr1:46036200-46047600	Weak transcription	Primary B cells from cord blood	blood
10	chr1:46036200-46048800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:46036400-46048000	Weak transcription	Spleen	Spleen
12	chr1:46036400-46048600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:46036400-46048800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:46036400-46048800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:46036400-46049200	Weak transcription	Gastric	stomach
16	chr1:46036600-46047400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:46036600-46048200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:46036600-46048600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:46036600-46048600	Weak transcription	Lung	lung
20	chr1:46036600-46048800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:46036600-46048800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:46036600-46048800	Weak transcription	Fetal Kidney	kidney
23	chr1:46036600-46048800	Weak transcription	Fetal Lung	lung
24	chr1:46036600-46048800	Weak transcription	Dnd41	blood
25	chr1:46036600-46048800	Weak transcription	HepG2	liver
26	chr1:46036800-46047600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:46036800-46047600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:46036800-46047600	Weak transcription	GM12878-XiMat	blood
29	chr1:46036800-46048000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:46036800-46048000	Weak transcription	Fetal Thymus	thymus
31	chr1:46036800-46048800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:46036800-46048800	Weak transcription	Adipose Nuclei	Adipose
33	chr1:46036800-46048800	Weak transcription	Liver	Liver
34	chr1:46036800-46048800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:46036800-46048800	Weak transcription	Fetal Brain Female	brain
36	chr1:46036800-46048800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:46036800-46048800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:46036800-46048800	Weak transcription	Thymus	Thymus
39	chr1:46036800-46048800	Weak transcription	A549	lung
40	chr1:46036800-46048800	Weak transcription	NH-A	brain
41	chr1:46036800-46048800	Weak transcription	Osteobl	bone
42	chr1:46036800-46049000	Weak transcription	Primary T cells from cord blood	blood
43	chr1:46036800-46049200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:46037000-46048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:46037200-46048800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:46037400-46047600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:46037400-46048600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:46037400-46048600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:46037400-46048800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:46037400-46048800	Weak transcription	Fetal Intestine Large	intestine

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