Variant report

Variant	rs6796362
Chromosome Location	chr3:105579227-105579228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105578910..105582345-chr3:105586229..105588462,4	MCF-7	breast:
2	chr3:105577086..105579511-chr3:105584750..105588658,3	K562	blood:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485832	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487841	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496588	0.87[AMR][1000 genomes]
rs2089092	0.82[AMR][1000 genomes]
rs2455887	0.86[ASN][1000 genomes]
rs3772512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344829	0.85[AMR][1000 genomes]
rs58882222	0.86[ASN][1000 genomes]
rs6437623	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791765	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793018	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997629	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997684	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639888	0.80[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs7650147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841798	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs9880744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105543400-105581200	Weak transcription	Gastric	stomach
2	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
4	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:105562000-105586000	Weak transcription	K562	blood
8	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
11	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:105565600-105584800	Weak transcription	NHEK	skin
14	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:105566600-105581200	Weak transcription	Aorta	Aorta
17	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
18	chr3:105567000-105583000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
25	chr3:105568600-105579600	Strong transcription	Osteobl	bone
26	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
27	chr3:105569400-105584000	Weak transcription	A549	lung
28	chr3:105569600-105579600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:105570200-105584200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:105570600-105584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:105571000-105582200	Weak transcription	Brain Germinal Matrix	brain
33	chr3:105571200-105584600	Weak transcription	NHLF	lung
34	chr3:105572000-105586200	Weak transcription	Lung	lung
35	chr3:105572200-105581200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:105572200-105584200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:105572200-105584600	Weak transcription	HSMMtube	muscle
38	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
39	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:105572400-105582800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:105572400-105583000	Weak transcription	HMEC	breast
42	chr3:105572600-105580400	Weak transcription	Fetal Heart	heart
43	chr3:105572600-105582800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:105572600-105582800	Weak transcription	Dnd41	blood
45	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
47	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:105573200-105581000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:105573200-105585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:105573400-105579400	Weak transcription	Rectal Mucosa Donor 31	rectum

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