Variant report

Variant	rs3819667
Chromosome Location	chr22:34226412-34226413
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34226044..34229431-chr22:34231299..34234951,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1009385	0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11089631	0.81[CHB][hapmap]
rs11089633	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11703278	0.82[CHB][hapmap]
rs11705248	0.81[CHB][hapmap]
rs12483818	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13053313	0.81[CHB][hapmap]
rs13053314	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13058342	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16993143	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16993180	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2267293	0.81[CHB][hapmap]
rs2267294	0.81[CHB][hapmap]
rs2267298	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs2267299	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267301	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283949	0.82[CHB][hapmap]
rs2283950	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34573078	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3827344	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4820113	0.82[CHB][hapmap]
rs4820120	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67503539	0.81[ASN][1000 genomes]
rs67714362	0.81[ASN][1000 genomes]
rs68063018	0.81[ASN][1000 genomes]
rs762836	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv459878	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv588936	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1064781	chr22:34152145-34231792	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv529886	chr22:34153740-34258847	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3819667	LARGE	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34200600-34234200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr22:34213000-34228000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr22:34213200-34232200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:34216800-34227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:34219800-34227400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:34219800-34228400	Weak transcription	Esophagus	oesophagus
7	chr22:34219800-34231800	Weak transcription	Aorta	Aorta
8	chr22:34220000-34227800	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:34220000-34228000	Weak transcription	Stomach Mucosa	stomach
10	chr22:34220000-34228400	Weak transcription	Brain Substantia Nigra	brain
11	chr22:34220600-34227800	Weak transcription	Ovary	ovary
12	chr22:34221000-34227800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr22:34221200-34231400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr22:34221600-34228600	Weak transcription	Liver	Liver
15	chr22:34221800-34228400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr22:34222000-34226600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr22:34222000-34227800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr22:34222200-34227800	Weak transcription	Brain Angular Gyrus	brain
19	chr22:34222200-34231200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:34224200-34228400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr22:34224400-34227600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr22:34224800-34229600	Enhancers	Fetal Heart	heart
23	chr22:34224800-34232000	Weak transcription	Fetal Intestine Small	intestine
24	chr22:34225000-34229000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr22:34225200-34228200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr22:34225200-34228800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr22:34225200-34229000	Enhancers	Left Ventricle	heart
28	chr22:34225200-34229200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr22:34225400-34226600	Enhancers	HSMMtube	muscle
30	chr22:34225600-34228000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr22:34225600-34228400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:34225600-34228600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:34225600-34228600	Enhancers	Spleen	Spleen
34	chr22:34225600-34229000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:34225600-34229000	Enhancers	Lung	lung
36	chr22:34225800-34226600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr22:34225800-34226600	Enhancers	Pancreas	Pancrea
38	chr22:34225800-34226800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr22:34225800-34228400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr22:34225800-34228400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr22:34225800-34228600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr22:34225800-34228600	Enhancers	Right Atrium	heart
43	chr22:34225800-34228800	Enhancers	Fetal Stomach	stomach
44	chr22:34225800-34229200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr22:34225800-34229600	Enhancers	Right Ventricle	heart
46	chr22:34226000-34226600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:34226200-34226600	Enhancers	Brain Hippocampus Middle	brain
48	chr22:34226200-34226800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr22:34226200-34226800	Enhancers	Gastric	stomach
50	chr22:34226200-34227400	Weak transcription	Psoas Muscle	Psoas

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