Variant report

Variant	rs3219487
Chromosome Location	chr1:45798555-45798556
allele	A/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	POLR2A	chr1:45798488-45798617	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45476992..45479513-chr1:45797519..45802277,7	K562	blood:
2	chr1:45195157..45197018-chr1:45796220..45798837,2	K562	blood:

Variant related genes	Relation type
MUTYH	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12042481	1.00[MEX][hapmap]
rs12568844	0.80[ASN][1000 genomes]
rs3219479	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3219493	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518315	0.81[AFR][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
rs3219487	CCDC163P	cis	Muscle Skeletal	GTEx
rs3219487	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs3219487	CCDC163P	cis	Whole Blood	GTEx
rs3219487	CCDC163P	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45792400-45800600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
3	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
4	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:45793400-45803800	Weak transcription	Small Intestine	intestine
6	chr1:45793400-45804000	Weak transcription	HMEC	breast
7	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
8	chr1:45793600-45800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:45793600-45800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45793600-45803600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:45793600-45803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
13	chr1:45793800-45799800	Weak transcription	HUVEC	blood vessel
14	chr1:45793800-45803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:45794000-45799600	Weak transcription	Fetal Heart	heart
16	chr1:45794000-45800000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:45794000-45800200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:45794000-45800600	Strong transcription	Fetal Stomach	stomach
19	chr1:45794200-45799800	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:45794400-45799600	Strong transcription	Brain Substantia Nigra	brain
21	chr1:45794400-45799800	Strong transcription	Brain Hippocampus Middle	brain
22	chr1:45794400-45799800	Strong transcription	Lung	lung
23	chr1:45794400-45800000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:45794400-45800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:45794400-45800400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr1:45794400-45800600	Strong transcription	Aorta	Aorta
27	chr1:45794400-45800800	Strong transcription	Fetal Brain Female	brain
28	chr1:45794600-45799600	Strong transcription	Fetal Intestine Small	intestine
29	chr1:45794600-45799600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:45794600-45799800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:45794600-45800000	Strong transcription	Primary T cells from cord blood	blood
32	chr1:45794600-45800400	Strong transcription	Pancreas	Pancrea
33	chr1:45794600-45800600	Strong transcription	Thymus	Thymus
34	chr1:45794800-45800200	Strong transcription	Brain Germinal Matrix	brain
35	chr1:45794800-45801200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:45795000-45799400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:45795000-45799600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:45795000-45799600	Strong transcription	Fetal Intestine Large	intestine
39	chr1:45795000-45799800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:45795000-45799800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:45795000-45799800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:45795000-45799800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:45795000-45800000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:45795000-45800000	Strong transcription	Liver	Liver
45	chr1:45795000-45800200	Strong transcription	Ovary	ovary
46	chr1:45795000-45800600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:45795000-45800600	Strong transcription	Dnd41	blood
48	chr1:45795200-45799400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:45795200-45799400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:45795200-45799600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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