Variant report

Variant	rs558068
Chromosome Location	chr17:38563710-38563711
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38563221..38564956-chr17:38570311..38572102,2	MCF-7	breast:
2	chr17:38557713..38559531-chr17:38562464..38565260,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1530363	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1662574	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16965783	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2586112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715556	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2715557	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473198	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs474510	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs477220	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs495511	0.86[EUR][1000 genomes]
rs505633	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506728	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507564	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs510336	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517047	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs525217	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs525812	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs528045	0.85[EUR][1000 genomes]
rs532299	0.94[ASN][1000 genomes]
rs552857	0.89[EUR][1000 genomes]
rs557498	0.89[EUR][1000 genomes]
rs62066565	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
2	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
3	chr17:38542200-38571600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:38542600-38566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr17:38542600-38566400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr17:38542600-38571800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:38543000-38566000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr17:38543200-38571000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:38543400-38571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:38543400-38571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:38543400-38571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:38543800-38566000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:38543800-38566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:38543800-38566400	Weak transcription	Fetal Heart	heart
15	chr17:38544000-38566600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr17:38544000-38566800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr17:38544000-38569800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:38544000-38570200	Strong transcription	HepG2	liver
19	chr17:38544000-38571800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:38544200-38567000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:38544400-38566600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr17:38544400-38573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:38545200-38573200	Weak transcription	Gastric	stomach
24	chr17:38546000-38573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:38546400-38572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr17:38546400-38572800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:38546400-38573200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:38547800-38565200	Weak transcription	Esophagus	oesophagus
29	chr17:38548200-38572000	Weak transcription	Brain Germinal Matrix	brain
30	chr17:38548400-38572800	Weak transcription	Primary B cells from cord blood	blood
31	chr17:38549800-38573000	Weak transcription	Fetal Intestine Large	intestine
32	chr17:38551000-38573000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr17:38552200-38564000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:38552200-38573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:38554200-38570400	Strong transcription	HMEC	breast
36	chr17:38554600-38569600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr17:38555600-38571000	Strong transcription	HUVEC	blood vessel
38	chr17:38556000-38568600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:38557400-38572800	Weak transcription	Fetal Kidney	kidney
40	chr17:38557600-38564600	Strong transcription	Thymus	Thymus
41	chr17:38557600-38571800	Weak transcription	Fetal Brain Female	brain
42	chr17:38557800-38572800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr17:38559000-38571600	Weak transcription	NHLF	lung
44	chr17:38559200-38573000	Weak transcription	Primary T cells from cord blood	blood
45	chr17:38559200-38573200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:38559400-38570400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:38559400-38571400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:38559400-38573200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr17:38559800-38572800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr17:38560400-38570200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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