Variant report

Variant	rs6804152
Chromosome Location	chr3:105583039-105583040
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: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1021858	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021859	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1039544	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511246	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11921710	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11924742	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633854	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1503921	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867192	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1910499	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2089091	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2197209	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4447799	0.81[EUR][1000 genomes]
rs4894840	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57520912	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58340800	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6437620	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6437621	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6437626	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767627	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619449	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629357	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7634844	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647955	0.81[EUR][1000 genomes]
rs7648842	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7649466	0.85[AMR][1000 genomes]
rs9631436	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9657904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826886	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9841500	0.81[EUR][1000 genomes]
rs9846534	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9869648	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874600	0.96[AMR][1000 genomes];0.90[EUR][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:122 , 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	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
21	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
22	chr3:105569400-105584000	Weak transcription	A549	lung
23	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:105570200-105584200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:105570600-105584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:105571200-105584600	Weak transcription	NHLF	lung
27	chr3:105572000-105586200	Weak transcription	Lung	lung
28	chr3:105572200-105584200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:105572200-105584600	Weak transcription	HSMMtube	muscle
30	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
31	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
34	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:105573200-105585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:105573400-105584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:105577000-105584000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:105577800-105583600	Strong transcription	Fetal Intestine Large	intestine
39	chr3:105579400-105584600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:105579400-105584800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:105579400-105585000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:105579600-105584200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:105579800-105585600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:105579800-105585800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:105580400-105583600	Strong transcription	HSMM	muscle
46	chr3:105580400-105584600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:105580400-105584600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:105580400-105584600	Enhancers	Fetal Heart	heart
49	chr3:105580600-105583200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:105581000-105583400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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