Variant report

Variant	rs3219479
Chromosome Location	chr1:45802143-45802144
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:45801371-45802149	HepG2	liver:	n/a	n/a
2	SP1	chr1:45801459-45802156	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45282552..45287322-chr1:45800975..45809178,15	K562	blood:
2	chr1:45476992..45479513-chr1:45797519..45802277,7	K562	blood:
3	chr1:45768110..45772204-chr1:45801230..45805942,7	MCF-7	breast:

Variant related genes	Relation type
TOE1	TF binding region
MUTYH	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12568844	0.80[ASN][1000 genomes]
rs3219487	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3219493	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[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	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	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3219479	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs3219479	CCDC163P	cis	lung	GTEx
rs3219479	CCDC163P	cis	Whole Blood	GTEx
rs3219479	CCDC163P	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
2	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
3	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:45793400-45803800	Weak transcription	Small Intestine	intestine
5	chr1:45793400-45804000	Weak transcription	HMEC	breast
6	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
7	chr1:45793600-45803600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45793600-45803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
10	chr1:45793800-45803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:45795600-45804400	Weak transcription	A549	lung
12	chr1:45795600-45804800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:45795800-45804600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:45796200-45803400	Weak transcription	K562	blood
15	chr1:45796400-45804600	Weak transcription	Hela-S3	cervix
16	chr1:45798200-45804400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:45798200-45804600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:45799000-45804600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:45799400-45803600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:45799400-45804600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:45799600-45803600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:45799600-45804200	Weak transcription	Osteobl	bone
23	chr1:45799600-45804400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:45799600-45804600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:45799800-45804600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:45799800-45804600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:45799800-45804600	Weak transcription	Fetal Lung	lung
28	chr1:45799800-45804600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:45799800-45804600	Weak transcription	HSMM	muscle
30	chr1:45799800-45804600	Weak transcription	NHLF	lung
31	chr1:45800000-45804400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:45800000-45804400	Enhancers	Stomach Mucosa	stomach
33	chr1:45800000-45804600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:45800000-45804600	Enhancers	Fetal Intestine Large	intestine
35	chr1:45800000-45804800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:45800200-45802600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:45800200-45802800	Enhancers	Duodenum Mucosa	Duodenum
38	chr1:45800200-45803600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:45800200-45803600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:45800200-45803600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:45800200-45803800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:45800200-45803800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:45800200-45804400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:45800200-45804400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:45800200-45804400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:45800200-45804400	Weak transcription	Brain Germinal Matrix	brain
47	chr1:45800200-45804400	Weak transcription	Fetal Heart	heart
48	chr1:45800200-45804400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:45800200-45804600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:45800200-45804600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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