Variant report

Variant	rs57504517
Chromosome Location	chr19:38202414-38202415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38202254..38204026-chr19:38208525..38211394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198182	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10153500	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10424047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878261	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11879149	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11880056	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11880604	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11883255	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34206817	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34743484	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3810359	0.80[ASN][1000 genomes]
rs45505797	0.83[EUR][1000 genomes]
rs56075341	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56264690	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56281742	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57725815	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57867853	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59966837	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60686304	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108260	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108262	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108264	0.80[ASN][1000 genomes]
rs62108289	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108290	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108292	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108293	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108297	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108302	0.81[ASN][1000 genomes]
rs62108344	0.93[AFR][1000 genomes]
rs62108348	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108350	0.95[ASN][1000 genomes]
rs62108354	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110178	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62110183	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62110185	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62110186	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62110187	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62110188	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62111488	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62111490	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245981	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246147	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7247175	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7247345	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7258992	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259029	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259717	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73932955	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8101476	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8101991	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102189	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8104124	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104747	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8108261	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184400-38208800	Weak transcription	HepG2	liver
3	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38187400-38205800	Strong transcription	Dnd41	blood
6	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
11	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
12	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
13	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
14	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
15	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:38192200-38203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
19	chr19:38194000-38203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:38194200-38202800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:38194600-38206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:38195200-38204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:38196000-38203000	ZNF genes & repeats	Liver	Liver
24	chr19:38196000-38204200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38196200-38202600	Strong transcription	Left Ventricle	heart
26	chr19:38196200-38204400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr19:38196800-38202800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:38197000-38203000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:38197000-38203000	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr19:38197200-38202800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:38197200-38203000	Strong transcription	Fetal Muscle Leg	muscle
32	chr19:38197200-38203400	Strong transcription	Primary T cells from cord blood	blood
33	chr19:38197400-38202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:38197600-38208800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:38198400-38202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:38198400-38202600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:38198600-38204400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
38	chr19:38198800-38203400	Strong transcription	Ovary	ovary
39	chr19:38198800-38208800	Weak transcription	Fetal Brain Male	brain
40	chr19:38198800-38209000	Weak transcription	Spleen	Spleen
41	chr19:38198800-38209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:38198800-38209200	Weak transcription	Gastric	stomach
43	chr19:38198800-38209400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:38198800-38209800	Weak transcription	Esophagus	oesophagus
45	chr19:38199000-38209000	Weak transcription	Fetal Kidney	kidney
46	chr19:38199000-38209000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:38199000-38209200	Weak transcription	Pancreas	Pancrea
48	chr19:38199000-38209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:38199000-38209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38199000-38209400	Weak transcription	HSMM	muscle

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