Variant report

Variant	rs62258160
Chromosome Location	chr3:105583438-105583439
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	chr3:105579577..105582453-chr3:105582537..105585477,2	MCF-7	breast:
2	chr3:105581787..105584079-chr3:105585457..105588306,3	K562	blood:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12054270	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487349	0.82[ASN][1000 genomes]
rs12493071	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443100	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503923	0.98[AMR][1000 genomes]
rs16851512	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851553	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851673	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851705	0.98[AMR][1000 genomes]
rs16851706	0.98[AMR][1000 genomes]
rs16851707	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814078	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867194	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028598	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028599	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055559	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120104	0.88[ASN][1000 genomes]
rs2301028	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301034	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301035	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213928	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34360428	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35909361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772517	0.90[ASN][1000 genomes]
rs3772522	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772525	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821490	0.88[ASN][1000 genomes]
rs4431143	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4469007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894956	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255571	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255572	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255573	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255575	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256353	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261460	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261462	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261487	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261489	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261491	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261492	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261493	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261495	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261496	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261497	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261498	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261499	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261538	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261539	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263056	0.87[ASN][1000 genomes]
rs62263057	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263059	0.87[ASN][1000 genomes]
rs62263169	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263170	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264260	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6809776	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619706	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628896	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631219	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641527	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650046	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964173	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9657903	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657924	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971109	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849559	0.88[ASN][1000 genomes]
rs9856147	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
3	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:105562000-105586000	Weak transcription	K562	blood
7	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:105565600-105584800	Weak transcription	NHEK	skin
12	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
15	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
20	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
21	chr3:105569400-105584000	Weak transcription	A549	lung
22	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:105570200-105584200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:105570600-105584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:105571200-105584600	Weak transcription	NHLF	lung
26	chr3:105572000-105586200	Weak transcription	Lung	lung
27	chr3:105572200-105584200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:105572200-105584600	Weak transcription	HSMMtube	muscle
29	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
30	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
33	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:105573200-105585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:105573400-105584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:105577000-105584000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:105577800-105583600	Strong transcription	Fetal Intestine Large	intestine
38	chr3:105579400-105584600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:105579400-105584800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:105579400-105585000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:105579600-105584200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:105579800-105585600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:105579800-105585800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:105580400-105583600	Strong transcription	HSMM	muscle
45	chr3:105580400-105584600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:105580400-105584600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:105580400-105584600	Enhancers	Fetal Heart	heart
48	chr3:105581000-105583600	Enhancers	Stomach Mucosa	stomach
49	chr3:105581000-105584000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:105581400-105583600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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