Variant report

Variant	rs11657628
Chromosome Location	chr17:46045923-46045924
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	FOSL1	chr17:46044883-46045964	HCT-116	colon:	n/a	chr17:46045561-46045571 chr17:46045561-46045571 chr17:46045548-46045559 chr17:46045561-46045571 chr17:46045296-46045305 chr17:46045561-46045571 chr17:46045550-46045561

No.	Distal block	Cell Line	Cell type
1	chr17:45917724..45920476-chr17:46044625..46046608,2	MCF-7	breast:
2	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
3	chr17:45917404..45919085-chr17:46045221..46048078,2	K562	blood:
4	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
5	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
6	chr17:46018061..46020719-chr17:46045036..46046879,2	K562	blood:
7	chr17:46043414..46046355-chr17:46124548..46126704,2	MCF-7	breast:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000141295	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1043603	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11654627	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11657628	SKAP1	cis	brain	BrainEAC

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
11	chr17:46037800-46047400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:46037800-46047400	Enhancers	Fetal Intestine Small	intestine
13	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
14	chr17:46038000-46046400	Weak transcription	K562	blood
15	chr17:46039600-46047600	Weak transcription	Primary T cells from cord blood	blood
16	chr17:46042800-46047800	Weak transcription	Small Intestine	intestine
17	chr17:46043000-46046400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:46043000-46047800	Enhancers	Pancreas	Pancrea
19	chr17:46043000-46047800	Enhancers	Stomach Mucosa	stomach
20	chr17:46043200-46046400	Weak transcription	Gastric	stomach
21	chr17:46043600-46046000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:46044200-46047600	Weak transcription	Liver	Liver
23	chr17:46044800-46046000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr17:46044800-46047000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:46044800-46047200	Enhancers	Duodenum Mucosa	Duodenum
26	chr17:46044800-46048000	Enhancers	Placenta	Placenta
27	chr17:46045000-46047800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr17:46045200-46047200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr17:46045200-46047600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:46045200-46047600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr17:46045400-46046200	Weak transcription	Colonic Mucosa	Colon
32	chr17:46045400-46047200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:46045400-46047400	Weak transcription	Colon Smooth Muscle	Colon
34	chr17:46045400-46047600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:46045400-46047600	Weak transcription	HSMM	muscle
36	chr17:46045400-46047800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:46045400-46047800	Weak transcription	Lung	lung
38	chr17:46045400-46048400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:46045600-46046000	Enhancers	Hela-S3	cervix
40	chr17:46045600-46046600	Enhancers	A549	lung
41	chr17:46045600-46047200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:46045600-46047200	Weak transcription	Esophagus	oesophagus
43	chr17:46045600-46047400	Weak transcription	HepG2	liver
44	chr17:46045600-46047600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:46045600-46047600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:46045600-46047600	Weak transcription	Osteobl	bone
47	chr17:46045600-46047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:46045800-46047200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:46045800-46047400	Weak transcription	HMEC	breast
50	chr17:46045800-46047600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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