Variant report

Variant	rs12554335
Chromosome Location	chr9:19108827-19108828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1042936	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17238021	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs2171957	0.86[JPT][hapmap]
rs41269009	0.88[AMR][1000 genomes]
rs41269011	0.88[AMR][1000 genomes]
rs4645631	0.84[CEU][hapmap]
rs4977494	0.84[CEU][hapmap];0.87[GIH][hapmap];0.92[MKK][hapmap]
rs4977495	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs4977496	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4977497	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7037156	0.84[CEU][hapmap]
rs9406759	1.00[CEU][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1018947	chr9:19094894-19394712	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
9	nsv1033552	chr9:19104662-19131866	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12554335	RRAGA	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19103000-19113800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:19103400-19110000	Weak transcription	Fetal Stomach	stomach
3	chr9:19103400-19111800	Weak transcription	Left Ventricle	heart
4	chr9:19103400-19114000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:19103400-19114000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:19103400-19114000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:19103400-19114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:19103400-19114200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:19103400-19114200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:19103400-19114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:19103400-19114400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:19103400-19114400	Weak transcription	Lung	lung
13	chr9:19103400-19114600	Weak transcription	NHLF	lung
14	chr9:19103400-19114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:19103400-19114800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:19103400-19114800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:19103400-19114800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:19103400-19114800	Weak transcription	Brain Substantia Nigra	brain
19	chr9:19103400-19114800	Weak transcription	HSMM	muscle
20	chr9:19103400-19114800	Weak transcription	NHDF-Ad	bronchial
21	chr9:19103400-19115000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:19103400-19115400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:19103400-19115600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:19103400-19115600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:19103400-19115600	Weak transcription	Fetal Lung	lung
26	chr9:19103400-19115600	Weak transcription	Ovary	ovary
27	chr9:19103400-19115800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:19103400-19115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:19103400-19115800	Weak transcription	Gastric	stomach
30	chr9:19103400-19116000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:19103400-19116000	Weak transcription	Brain Germinal Matrix	brain
32	chr9:19103400-19116000	Weak transcription	Small Intestine	intestine
33	chr9:19103400-19116200	Weak transcription	Aorta	Aorta
34	chr9:19103400-19116200	Weak transcription	Esophagus	oesophagus
35	chr9:19103400-19120200	Weak transcription	Pancreas	Pancrea
36	chr9:19103400-19126400	Weak transcription	Fetal Brain Male	brain
37	chr9:19103600-19111400	Weak transcription	Adipose Nuclei	Adipose
38	chr9:19103600-19113800	Weak transcription	Fetal Intestine Small	intestine
39	chr9:19103600-19114000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:19103600-19114000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:19103600-19114000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:19103600-19114000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:19103600-19114000	Weak transcription	Fetal Intestine Large	intestine
44	chr9:19103600-19114000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:19103600-19114000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:19103600-19114000	Weak transcription	Right Ventricle	heart
47	chr9:19103600-19114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:19103600-19114200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:19103600-19114400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:19103600-19114400	Weak transcription	Primary monocytes fromperipheralblood	blood

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