Variant report

Variant	rs5749679
Chromosome Location	chr22:34229105-34229106
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	chr22:34226044..34229431-chr22:34231299..34234951,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12484737	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs16993156	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17809399	0.97[GIH][hapmap]
rs2018285	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2253063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267306	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs2283952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749677	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs5749680	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754715	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754717	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754731	0.89[GIH][hapmap]
rs5999123	0.97[GIH][hapmap]
rs738949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5749679	CABP7	cis	parietal	SCAN
rs5749679	HSCB	cis	parietal	SCAN

Chromatin state (count:59 , 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	chr22:34213200-34232200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:34219800-34231800	Weak transcription	Aorta	Aorta
4	chr22:34221200-34231400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr22:34222200-34231200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr22:34224800-34229600	Enhancers	Fetal Heart	heart
7	chr22:34224800-34232000	Weak transcription	Fetal Intestine Small	intestine
8	chr22:34225200-34229200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr22:34225800-34229200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr22:34225800-34229600	Enhancers	Right Ventricle	heart
11	chr22:34226600-34246200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr22:34226800-34229400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr22:34227200-34229600	Enhancers	Gastric	stomach
14	chr22:34227600-34229600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr22:34228000-34229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr22:34228000-34229200	Enhancers	Stomach Mucosa	stomach
17	chr22:34228000-34230600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:34228200-34230800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr22:34228200-34231400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr22:34228400-34230200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:34228400-34230600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr22:34228400-34230800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr22:34228400-34230800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:34228400-34231400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr22:34228600-34230000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr22:34228600-34230800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:34228600-34230800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr22:34228600-34231000	Weak transcription	Fetal Brain Male	brain
29	chr22:34228600-34231000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr22:34228600-34231400	Weak transcription	Brain Angular Gyrus	brain
31	chr22:34228600-34231400	Weak transcription	Right Atrium	heart
32	chr22:34228600-34232200	Weak transcription	Spleen	Spleen
33	chr22:34228600-34234000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:34228600-34234800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:34228800-34229200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr22:34228800-34230000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr22:34228800-34230800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr22:34228800-34230800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:34228800-34230800	Weak transcription	Fetal Stomach	stomach
40	chr22:34228800-34231000	Weak transcription	Colon Smooth Muscle	Colon
41	chr22:34228800-34231200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:34228800-34231400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr22:34228800-34231400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr22:34228800-34231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr22:34228800-34240000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr22:34229000-34231200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:34229000-34231200	Weak transcription	Brain Hippocampus Middle	brain
48	chr22:34229000-34231200	Weak transcription	Fetal Muscle Leg	muscle
49	chr22:34229000-34231200	Weak transcription	Psoas Muscle	Psoas
50	chr22:34229000-34231400	Weak transcription	Colonic Mucosa	Colon

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