Variant report

Variant	rs17504298
Chromosome Location	chr1:225883399-225883400
allele	C/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	SETDB1	chr1:225881827-225883517	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227496	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10915856	0.80[AFR][1000 genomes]
rs17569722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653425	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653426	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653647	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653648	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55965048	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260304	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60377022	0.89[AFR][1000 genomes]
rs6694288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753075	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73125729	0.89[AFR][1000 genomes]
rs7366333	0.81[AMR][1000 genomes]
rs7521926	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17504298	SNAP47	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225865600-225888000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:225875200-225898600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:225878600-225884000	Enhancers	Right Atrium	heart
4	chr1:225878600-225885400	Enhancers	Left Ventricle	heart
5	chr1:225879000-225884200	Enhancers	Liver	Liver
6	chr1:225879000-225884400	Enhancers	HepG2	liver
7	chr1:225879400-225887000	Weak transcription	NHLF	lung
8	chr1:225880400-225884200	Enhancers	A549	lung
9	chr1:225880800-225887800	Weak transcription	Spleen	Spleen
10	chr1:225881000-225883800	Weak transcription	Psoas Muscle	Psoas
11	chr1:225881000-225887200	Weak transcription	Right Ventricle	heart
12	chr1:225881800-225884200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:225881800-225884200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:225881800-225885600	Enhancers	Fetal Stomach	stomach
15	chr1:225882000-225883600	Enhancers	Fetal Intestine Small	intestine
16	chr1:225882000-225884200	Enhancers	Aorta	Aorta
17	chr1:225882000-225884600	Enhancers	Pancreas	Pancrea
18	chr1:225882000-225885400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:225882000-225885600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:225882200-225887000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:225882200-225889600	Enhancers	Fetal Muscle Leg	muscle
22	chr1:225882400-225883400	Weak transcription	Fetal Heart	heart
23	chr1:225882400-225883400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:225882400-225887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:225882400-225887000	Weak transcription	Hela-S3	cervix
26	chr1:225882400-225887200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:225882400-225887200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:225882400-225908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:225882600-225884000	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:225882800-225883600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:225882800-225884000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:225882800-225887000	Weak transcription	Stomach Mucosa	stomach
33	chr1:225883000-225883600	Enhancers	NHEK	skin
34	chr1:225883000-225883800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:225883000-225883800	Weak transcription	Ovary	ovary
36	chr1:225883000-225884000	Enhancers	Colon Smooth Muscle	Colon
37	chr1:225883000-225884000	Weak transcription	Placenta	Placenta
38	chr1:225883000-225884000	Enhancers	NHDF-Ad	bronchial
39	chr1:225883000-225884400	Enhancers	Osteobl	bone
40	chr1:225883000-225885200	Weak transcription	Lung	lung
41	chr1:225883000-225887000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:225883000-225887000	Weak transcription	HUVEC	blood vessel
43	chr1:225883000-225887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:225883200-225883400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:225883200-225883400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:225883200-225883400	Enhancers	Fetal Lung	lung
47	chr1:225883200-225884000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:225883200-225884000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:225883200-225884000	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:225883200-225884400	Enhancers	Fetal Kidney	kidney

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