Variant report

Variant	rs203478
Chromosome Location	chr17:19829842-19829843
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	chr17:19770914..19772634-chr17:19827559..19830080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12449662	0.83[AMR][1000 genomes]
rs12450857	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12453720	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12943369	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12944084	0.81[AMR][1000 genomes]
rs1638526	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1638527	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1638528	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs169413	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17604987	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17605101	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17668529	0.86[AMR][1000 genomes]
rs17759609	0.83[CEU][hapmap]
rs203449	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203454	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203464	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203467	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203474	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs203475	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203476	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203480	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2108981	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34182788	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34726000	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35315252	0.82[AMR][1000 genomes]
rs35925051	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35979784	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36097967	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs403021	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs427033	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925054	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925055	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4925063	0.85[AMR][1000 genomes]
rs4925064	0.86[AMR][1000 genomes]
rs56005410	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62066267	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62066345	0.83[AMR][1000 genomes]
rs62066346	0.81[AMR][1000 genomes]
rs62066347	0.81[AMR][1000 genomes]
rs62066348	0.86[AMR][1000 genomes]
rs62066349	0.86[AMR][1000 genomes]
rs62066350	0.86[AMR][1000 genomes]
rs62066351	0.86[AMR][1000 genomes]
rs6813	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7209653	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8079923	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs850622	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9891503	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9901294	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
5	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:19804000-19853000	Strong transcription	Dnd41	blood
11	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:19809200-19832200	Weak transcription	Fetal Brain Male	brain
17	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:19810000-19830800	Strong transcription	Adipose Nuclei	Adipose
19	chr17:19810200-19836600	Weak transcription	Fetal Heart	heart
20	chr17:19811800-19834800	Weak transcription	Small Intestine	intestine
21	chr17:19812200-19845400	Strong transcription	Liver	Liver
22	chr17:19813200-19833800	Weak transcription	Pancreas	Pancrea
23	chr17:19815000-19838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:19816800-19844400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:19817800-19844200	Weak transcription	Stomach Mucosa	stomach
26	chr17:19818200-19830600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:19818200-19836400	Strong transcription	A549	lung
28	chr17:19818600-19839400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:19819600-19833600	Weak transcription	Brain Substantia Nigra	brain
30	chr17:19819600-19844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:19819800-19833800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:19820000-19832200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:19821000-19831800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:19821000-19832200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr17:19821000-19833800	Weak transcription	Aorta	Aorta
36	chr17:19821000-19838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:19821000-19842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr17:19822000-19830200	Weak transcription	Lung	lung
39	chr17:19822000-19830200	Weak transcription	Spleen	Spleen
40	chr17:19822000-19832200	Weak transcription	Brain Angular Gyrus	brain
41	chr17:19822000-19832400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:19822000-19833600	Weak transcription	Gastric	stomach
43	chr17:19823000-19830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:19823000-19832200	Weak transcription	Brain Hippocampus Middle	brain
45	chr17:19823000-19832200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:19823000-19833600	Weak transcription	Brain Germinal Matrix	brain
47	chr17:19823000-19833800	Weak transcription	Esophagus	oesophagus
48	chr17:19823400-19833200	Weak transcription	NHLF	lung
49	chr17:19823400-19837600	Weak transcription	Psoas Muscle	Psoas
50	chr17:19823600-19830400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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