Variant report

Variant	rs17273898
Chromosome Location	chr9:13246519-13246520
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	chr9:13245657..13247575-chr9:13257459..13259209,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10756461	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10756465	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10809920	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10809924	0.82[CHB][hapmap]
rs1330129	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs4741291	0.91[JPT][hapmap]
rs6474759	0.82[CHB][hapmap]
rs7041374	0.82[CHB][hapmap]
rs72706378	0.87[EUR][1000 genomes]
rs7863888	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17273898	ZDHHC21	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13164200-13248600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:13164200-13258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:13189000-13268600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:13202800-13250600	Weak transcription	Pancreas	Pancrea
5	chr9:13202800-13250800	Weak transcription	Psoas Muscle	Psoas
6	chr9:13203000-13261000	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:13203400-13247000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:13204000-13249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:13206000-13247000	Weak transcription	Brain Angular Gyrus	brain
10	chr9:13208200-13265000	Weak transcription	Aorta	Aorta
11	chr9:13209800-13266000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:13216600-13247000	Weak transcription	Fetal Brain Female	brain
13	chr9:13219800-13265600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:13221800-13246600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:13224000-13264600	Weak transcription	Osteobl	bone
16	chr9:13224400-13252400	Weak transcription	Liver	Liver
17	chr9:13224600-13247000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:13226000-13252800	Weak transcription	Fetal Heart	heart
19	chr9:13226400-13247000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:13226600-13259200	Weak transcription	Right Ventricle	heart
21	chr9:13226800-13278000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:13229400-13247200	Weak transcription	HSMMtube	muscle
23	chr9:13232400-13264800	Weak transcription	NH-A	brain
24	chr9:13233800-13255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:13235800-13247200	Weak transcription	Brain Germinal Matrix	brain
26	chr9:13236400-13248000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:13236400-13264400	Weak transcription	Fetal Intestine Small	intestine
28	chr9:13236600-13251600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:13237400-13247000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:13238000-13264800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:13238400-13247600	Weak transcription	Lung	lung
32	chr9:13238400-13254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:13238600-13246800	Weak transcription	Adipose Nuclei	Adipose
34	chr9:13238600-13251200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:13240000-13278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:13240200-13253400	Weak transcription	Placenta	Placenta
37	chr9:13240200-13255600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:13240400-13247200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr9:13240400-13251400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:13240800-13263000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:13241200-13248000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:13241200-13251200	Weak transcription	NHLF	lung
43	chr9:13241400-13247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:13241600-13247800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:13241800-13249800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:13242800-13247200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:13242800-13253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:13243000-13247200	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:13243000-13247200	Weak transcription	Left Ventricle	heart
50	chr9:13243000-13255600	Weak transcription	Fetal Muscle Trunk	muscle

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