Variant report

Variant	rs475298
Chromosome Location	chr17:38654792-38654793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38597908..38601053-chr17:38654458..38659532,5	MCF-7	breast:
2	chr17:38654631..38657600-chr17:38717597..38719399,2	MCF-7	breast:
3	chr17:38653905..38655672-chr17:38666687..38669670,2	MCF-7	breast:
4	chr17:38653160..38655925-chr17:38703995..38706258,2	MCF-7	breast:
5	chr17:38653701..38656623-chr17:38703547..38705327,2	MCF-7	breast:
6	chr17:38650172..38654327-chr17:38654681..38657235,5	K562	blood:
7	chr17:38652390..38654327-chr17:38654701..38657049,2	K562	blood:
8	chr17:38645169..38647955-chr17:38652977..38654925,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1018953	1.00[JPT][hapmap]
rs11574663	1.00[JPT][hapmap]
rs2229095	1.00[JPT][hapmap]
rs28485796	0.88[ASN][1000 genomes]
rs3136687	1.00[JPT][hapmap]
rs3136689	1.00[JPT][hapmap]
rs3136694	1.00[JPT][hapmap]
rs3136695	1.00[JPT][hapmap]
rs4092050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4890086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4890087	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499490	1.00[CHB][hapmap]
rs594783	1.00[CHB][hapmap]
rs596960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs634299	1.00[ASN][1000 genomes]
rs6503543	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217539	0.82[CEU][hapmap]
rs7221799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896135	0.82[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs896136	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs921394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675320	1.00[JPT][hapmap]
rs9901908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912358	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38643800-38656000	Weak transcription	Right Atrium	heart
2	chr17:38647000-38655200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
3	chr17:38647000-38656000	Weak transcription	Lung	lung
4	chr17:38647000-38656200	Weak transcription	Gastric	stomach
5	chr17:38647200-38655600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:38647200-38656000	Weak transcription	Pancreas	Pancrea
7	chr17:38648200-38655800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:38648400-38654800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:38649600-38654800	Genic enhancers	Placenta	Placenta
10	chr17:38649600-38655200	Transcr. at gene 5' and 3'	A549	lung
11	chr17:38649600-38657600	Transcr. at gene 5' and 3'	NHEK	skin
12	chr17:38649800-38655400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:38652800-38655400	Weak transcription	Esophagus	oesophagus
14	chr17:38652800-38656000	Weak transcription	Spleen	Spleen
15	chr17:38653200-38655800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr17:38653600-38654800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:38653600-38654800	Flanking Active TSS	HMEC	breast
18	chr17:38653600-38655600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:38653600-38656600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:38653800-38654800	Enhancers	HSMM	muscle
21	chr17:38653800-38655000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr17:38653800-38655000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr17:38653800-38655200	Flanking Active TSS	Hela-S3	cervix
24	chr17:38653800-38655600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr17:38653800-38655600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr17:38653800-38655800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:38653800-38655800	Enhancers	Osteobl	bone
28	chr17:38653800-38656000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:38653800-38656400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr17:38653800-38656800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:38653800-38657000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:38653800-38657200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:38654000-38654800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr17:38654000-38655000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr17:38654000-38655000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:38654000-38655000	Enhancers	Small Intestine	intestine
37	chr17:38654000-38655200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:38654000-38655400	Enhancers	Stomach Smooth Muscle	stomach
39	chr17:38654000-38655600	Enhancers	Colon Smooth Muscle	Colon
40	chr17:38654200-38655000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr17:38654200-38655000	Enhancers	Stomach Mucosa	stomach
42	chr17:38654200-38655000	Enhancers	NHLF	lung
43	chr17:38654200-38655400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr17:38654200-38655600	Enhancers	HepG2	liver
45	chr17:38654200-38655800	Enhancers	Fetal Muscle Trunk	muscle
46	chr17:38654200-38655800	Enhancers	K562	blood
47	chr17:38654200-38656000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:38654200-38656600	Enhancers	NHDF-Ad	bronchial
49	chr17:38654200-38656800	Enhancers	Left Ventricle	heart
50	chr17:38654200-38657000	Enhancers	Right Ventricle	heart

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