Variant report

Variant	rs4890086
Chromosome Location	chr17:38652976-38652977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38474609..38477239-chr17:38652273..38654594,2	MCF-7	breast:
2	chr17:38650686..38654337-chr17:38656373..38659977,5	MCF-7	breast:
3	chr17:38645404..38649775-chr17:38650279..38653252,5	MCF-7	breast:
4	chr17:38651968..38654785-chr17:38673246..38675780,2	K562	blood:
5	chr17:38652390..38654327-chr17:38654701..38657049,2	K562	blood:
6	chr17:38650172..38654327-chr17:38654681..38657235,5	K562	blood:

Variant related genes	Relation type
ENSG00000266088	Chromatin interaction
ENSG00000131746	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1018953	1.00[JPT][hapmap]
rs11574663	1.00[JPT][hapmap]
rs2229095	1.00[JPT][hapmap]
rs28485796	0.83[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[CHB][hapmap]
rs475298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4890087	1.00[ASN][1000 genomes]
rs4890088	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs499490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs594783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs596960	1.00[CHB][hapmap]
rs634299	0.94[ASN][1000 genomes]
rs6503543	1.00[JPT][hapmap]
rs7212543	1.00[CEU][hapmap]
rs7221799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73310952	1.00[AMR][1000 genomes]
rs8066508	1.00[CEU][hapmap]
rs8069091	1.00[CEU][hapmap]
rs8077724	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs896136	1.00[JPT][hapmap]
rs921394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9675320	1.00[JPT][hapmap]
rs9901908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38642000-38654400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr17:38643000-38654200	Weak transcription	Stomach Mucosa	stomach
3	chr17:38643800-38656000	Weak transcription	Right Atrium	heart
4	chr17:38647000-38655200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
5	chr17:38647000-38656000	Weak transcription	Lung	lung
6	chr17:38647000-38656200	Weak transcription	Gastric	stomach
7	chr17:38647200-38654200	Weak transcription	Adipose Nuclei	Adipose
8	chr17:38647200-38654200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr17:38647200-38655600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:38647200-38656000	Weak transcription	Pancreas	Pancrea
11	chr17:38647600-38653800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:38647800-38654200	Weak transcription	K562	blood
13	chr17:38647800-38654400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:38648000-38654000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:38648000-38654600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:38648200-38654200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:38648200-38654200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:38648200-38655800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:38648400-38654000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:38648400-38654200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:38648400-38654800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:38648600-38653800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:38648600-38653800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:38648600-38654000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr17:38648600-38654400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr17:38649000-38654200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:38649400-38654200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:38649600-38654800	Genic enhancers	Placenta	Placenta
29	chr17:38649600-38655200	Transcr. at gene 5' and 3'	A549	lung
30	chr17:38649600-38657600	Transcr. at gene 5' and 3'	NHEK	skin
31	chr17:38649800-38655400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:38650200-38653600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:38650200-38654000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:38650200-38654000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:38650400-38653200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:38650400-38653800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:38650400-38654000	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:38650600-38653600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:38650600-38653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr17:38650600-38653800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:38650600-38653800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:38650600-38653800	Weak transcription	Osteobl	bone
43	chr17:38650600-38654200	Weak transcription	NHDF-Ad	bronchial
44	chr17:38651000-38653600	Transcr. at gene 5' and 3'	HMEC	breast
45	chr17:38651200-38654200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:38651400-38653200	Transcr. at gene 5' and 3'	Hela-S3	cervix
47	chr17:38652400-38653000	Enhancers	HepG2	liver
48	chr17:38652400-38653800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:38652600-38654200	Weak transcription	Colonic Mucosa	Colon
50	chr17:38652800-38653000	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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