Variant report

Variant	rs1475564
Chromosome Location	chr1:62579672-62579673
allele	G/T
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	MAFK	chr1:62579061-62579672	GM12878	blood:	n/a	chr1:62579367-62579383 chr1:62579367-62579378 chr1:62579367-62579382 chr1:62579370-62579386 chr1:62579368-62579388 chr1:62579371-62579385 chr1:62579368-62579379 chr1:62579366-62579380 chr1:62579367-62579378 chr1:62579368-62579379

Variant related genes	Relation type
INADL	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11207905	1.00[CHB][hapmap]
rs1475563	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs1475565	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs1475566	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961234	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476195	0.82[EUR][1000 genomes]
rs2476197	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2481667	0.81[EUR][1000 genomes]
rs2481672	0.82[TSI][hapmap]
rs2481683	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9436219	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1475564	INADL	cis	cerebellum	SCAN
rs1475564	TM2D1	cis	cerebellum	SCAN
rs1475564	ATG4C	cis	cerebellum	SCAN
rs1475564	IPP	trans	cerebellum	SCAN
rs1475564	KANK4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:62542400-62586800	Weak transcription	NHEK	skin
5	chr1:62542400-62587400	Weak transcription	HMEC	breast
6	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62548200-62594000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
10	chr1:62551800-62594200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
12	chr1:62553000-62582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:62553200-62594200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:62554400-62581600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:62555000-62589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:62555000-62594200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:62556000-62594200	Weak transcription	Left Ventricle	heart
19	chr1:62559600-62582000	Weak transcription	Liver	Liver
20	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:62566000-62593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:62566200-62582200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:62566200-62594400	Weak transcription	Aorta	Aorta
24	chr1:62566200-62603400	Weak transcription	Esophagus	oesophagus
25	chr1:62566200-62604400	Weak transcription	Lung	lung
26	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:62567200-62594200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:62569800-62594400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:62570000-62594400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:62575000-62587200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
34	chr1:62576600-62582600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:62576600-62593800	Weak transcription	Ovary	ovary
36	chr1:62576600-62594200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:62576600-62596800	Weak transcription	Fetal Stomach	stomach
38	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
39	chr1:62576800-62607800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:62577800-62580000	Strong transcription	Fetal Intestine Small	intestine
41	chr1:62578000-62579800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:62578000-62584600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:62578400-62581800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:62579000-62580800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:62579400-62581600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:62579600-62580000	Strong transcription	Gastric	stomach
47	chr1:62579600-62580000	Strong transcription	Pancreas	Pancrea
48	chr1:62579600-62580600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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