Variant report

Variant	rs2613320
Chromosome Location	chr9:93654090-93654091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs158508	1.00[CHB][hapmap]
rs1755958	1.00[CHB][hapmap]
rs1760124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1760125	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2035072	1.00[CHB][hapmap]
rs2613310	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs290203	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs290213	1.00[CHB][hapmap]
rs290224	0.93[ASN][1000 genomes]
rs290225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs290232	1.00[CHB][hapmap]
rs290234	1.00[CHB][hapmap]
rs290235	1.00[CHB][hapmap]
rs290236	1.00[CHB][hapmap]
rs290237	1.00[CHB][hapmap]
rs290238	1.00[CHB][hapmap]
rs290256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs290257	0.93[ASN][1000 genomes]
rs914929	1.00[JPT][hapmap]
rs965892	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2613320	GADD45G	cis	cerebellum	SCAN
rs2613320	CENPP	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93634000-93666200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:93641200-93657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:93643000-93666600	Weak transcription	Stomach Mucosa	stomach
4	chr9:93643200-93656800	Weak transcription	Small Intestine	intestine
5	chr9:93643200-93663400	Weak transcription	Adipose Nuclei	Adipose
6	chr9:93643600-93665400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:93646200-93664800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr9:93646800-93657000	Weak transcription	NHEK	skin
9	chr9:93647200-93663400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:93647400-93666600	Strong transcription	Primary B cells from cord blood	blood
11	chr9:93647600-93662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:93647600-93664800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:93647800-93654400	Strong transcription	Primary hematopoietic stem cells	blood
14	chr9:93647800-93662000	Strong transcription	Fetal Thymus	thymus
15	chr9:93648000-93662400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr9:93648200-93663200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:93648200-93665000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:93648600-93661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:93648800-93663200	Strong transcription	Thymus	Thymus
20	chr9:93650000-93660800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr9:93650000-93661200	Strong transcription	Fetal Intestine Small	intestine
22	chr9:93650000-93661400	Strong transcription	Fetal Stomach	stomach
23	chr9:93650000-93662600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr9:93651600-93655800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:93651600-93657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:93651600-93661600	Weak transcription	Fetal Kidney	kidney
27	chr9:93651600-93664200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:93652200-93654800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:93652200-93655400	Weak transcription	Liver	Liver
30	chr9:93652600-93654800	Weak transcription	Lung	lung
31	chr9:93652600-93655000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:93652600-93656800	Weak transcription	GM12878-XiMat	blood
33	chr9:93652600-93667200	Weak transcription	Gastric	stomach
34	chr9:93652800-93655400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr9:93652800-93655800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr9:93652800-93656000	Weak transcription	Pancreas	Pancrea
37	chr9:93652800-93657600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:93652800-93657600	Weak transcription	Colonic Mucosa	Colon
39	chr9:93653000-93658800	Weak transcription	Esophagus	oesophagus
40	chr9:93653200-93654600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:93653200-93655200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr9:93653200-93656000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:93653200-93657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr9:93653400-93656200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr9:93653400-93658000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:93653600-93656600	Strong transcription	Fetal Intestine Large	intestine
47	chr9:93653800-93655200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:93653800-93656200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:93654000-93654200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr9:93654000-93654200	Enhancers	H9 Cell Line	embryonic stem cell

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