Variant report

Variant	rs4924922
Chromosome Location	chr17:17430649-17430650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17398028..17400526-chr17:17429314..17431940,2	MCF-7	breast:
2	chr17:17412469..17415269-chr17:17430447..17432803,2	MCF-7	breast:
3	chr17:17419916..17424407-chr17:17429833..17432704,4	K562	blood:

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction
ENSG00000133027	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11651620	0.89[CEU][hapmap]
rs12935886	0.85[EUR][1000 genomes]
rs2168345	0.85[EUR][1000 genomes]
rs4244592	0.85[EUR][1000 genomes]
rs4244593	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4244594	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4646385	0.81[CEU][hapmap]
rs4646387	0.88[CEU][hapmap]
rs4646389	0.89[CEU][hapmap]
rs4646390	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4646391	0.88[CEU][hapmap]
rs4646392	0.88[CEU][hapmap]
rs4646397	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4646402	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs4646405	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs6502603	0.88[CEU][hapmap]
rs746899	0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs747770	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs748196	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs750546	0.82[CEU][hapmap]
rs8080165	0.81[EUR][1000 genomes]
rs8082417	0.81[CEU][hapmap]
rs936108	0.88[CEU][hapmap]
rs9892560	0.83[EUR][1000 genomes]
rs9894321	0.83[EUR][1000 genomes]
rs9894588	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv907742	chr17:17404586-17432744	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv907743	chr17:17404586-17448589	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv523094	chr17:17415217-17430649	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv907749	chr17:17417169-17448589	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv524158	chr17:17420199-17430649	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv574526	chr17:17422608-17444369	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
17	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924922	SNORD49B	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17413200-17437400	Weak transcription	Aorta	Aorta
2	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
3	chr17:17419400-17430800	Weak transcription	Placenta	Placenta
4	chr17:17419600-17447000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:17420600-17434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:17421000-17439200	Weak transcription	HSMM	muscle
7	chr17:17424600-17460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:17425000-17430800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:17425000-17431200	Weak transcription	Spleen	Spleen
10	chr17:17427000-17436200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:17427200-17440600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:17427400-17432400	Weak transcription	HepG2	liver
13	chr17:17427600-17432800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr17:17427600-17434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:17427800-17431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:17428200-17433200	Enhancers	Fetal Muscle Leg	muscle
17	chr17:17428400-17430800	Enhancers	Fetal Muscle Trunk	muscle
18	chr17:17428400-17432600	Enhancers	Adipose Nuclei	Adipose
19	chr17:17428600-17433800	Enhancers	Liver	Liver
20	chr17:17429000-17431000	Weak transcription	Gastric	stomach
21	chr17:17429000-17431200	Weak transcription	Right Atrium	heart
22	chr17:17429400-17432200	Enhancers	Fetal Stomach	stomach
23	chr17:17429400-17433200	Enhancers	Fetal Heart	heart
24	chr17:17429600-17431200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr17:17429800-17431600	Weak transcription	Fetal Intestine Small	intestine
26	chr17:17429800-17433000	Enhancers	Right Ventricle	heart
27	chr17:17430000-17431000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:17430000-17431000	Weak transcription	Left Ventricle	heart
29	chr17:17430000-17432600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr17:17430200-17431600	Weak transcription	Pancreas	Pancrea
31	chr17:17430200-17432200	Weak transcription	Stomach Mucosa	stomach
32	chr17:17430200-17438800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:17430200-17439200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr17:17430400-17430800	Weak transcription	Brain Germinal Matrix	brain
35	chr17:17430400-17430800	Weak transcription	Fetal Lung	lung
36	chr17:17430400-17430800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr17:17430400-17430800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr17:17430400-17431200	Weak transcription	Psoas Muscle	Psoas
39	chr17:17430400-17431400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:17430400-17431800	Weak transcription	Ovary	ovary
41	chr17:17430400-17432400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:17430600-17431600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:17430600-17432800	Enhancers	Lung	lung

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