Variant report

Variant	rs203454
Chromosome Location	chr17:19821513-19821514
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	chr10:133869109..133871241-chr17:19821449..19823085,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12450857	0.82[AMR][1000 genomes]
rs12453720	0.82[AMR][1000 genomes]
rs12943369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1638526	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1638527	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1638528	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17604987	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17605101	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17668529	0.81[AMR][1000 genomes]
rs203449	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203464	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203467	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203474	0.95[EUR][1000 genomes]
rs203475	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203476	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203478	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203480	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2108981	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34182788	0.81[AMR][1000 genomes]
rs34726000	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35925051	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36097967	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs403021	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs427033	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925054	0.82[AMR][1000 genomes]
rs4925055	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4925063	0.80[AMR][1000 genomes]
rs4925064	0.81[AMR][1000 genomes]
rs56005410	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62066267	0.82[AMR][1000 genomes]
rs62066348	0.81[AMR][1000 genomes]
rs62066349	0.81[AMR][1000 genomes]
rs62066350	0.81[AMR][1000 genomes]
rs62066351	0.81[AMR][1000 genomes]
rs6813	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209653	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8079923	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs850622	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9891503	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9901294	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
3	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:19803000-19822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:19803000-19824400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
9	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:19803600-19826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:19803800-19822400	Strong transcription	Primary T cells from cord blood	blood
15	chr17:19803800-19823400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr17:19803800-19824000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:19804000-19823600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:19804000-19853000	Strong transcription	Dnd41	blood
21	chr17:19805600-19823800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:19805800-19824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr17:19807000-19825800	Strong transcription	Placenta	Placenta
28	chr17:19807200-19823400	Strong transcription	Thymus	Thymus
29	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:19808000-19823600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:19808200-19828400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:19808400-19823000	Strong transcription	Brain Hippocampus Middle	brain
33	chr17:19808400-19823000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:19808400-19823800	Strong transcription	Fetal Lung	lung
35	chr17:19809200-19824000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:19809200-19832200	Weak transcription	Fetal Brain Male	brain
37	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:19809800-19828000	Weak transcription	K562	blood
39	chr17:19810000-19830800	Strong transcription	Adipose Nuclei	Adipose
40	chr17:19810200-19821600	Weak transcription	Gastric	stomach
41	chr17:19810200-19826200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr17:19810200-19826400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr17:19810200-19836600	Weak transcription	Fetal Heart	heart
44	chr17:19811000-19823400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:19811200-19824000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr17:19811600-19823200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:19811800-19834800	Weak transcription	Small Intestine	intestine
48	chr17:19812200-19845400	Strong transcription	Liver	Liver
49	chr17:19813200-19827200	Weak transcription	Colonic Mucosa	Colon
50	chr17:19813200-19828000	Weak transcription	H9 Cell Line	embryonic stem cell

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