Variant report

Variant	rs290256
Chromosome Location	chr9:93651615-93651616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs158508	1.00[CHB][hapmap]
rs1755958	1.00[CHB][hapmap]
rs1760124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1760125	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2035072	1.00[CHB][hapmap]
rs2613310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613320	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]
rs2774257	0.81[EUR][1000 genomes]
rs2780710	0.82[EUR][1000 genomes]
rs290203	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs290204	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs290213	1.00[CHB][hapmap]
rs290224	1.00[ASN][1000 genomes]
rs290225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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]
rs290257	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991216	0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs914928	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs914929	1.00[JPT][hapmap]
rs965892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs290256	SPTLC1	cis	cerebellum	SCAN
rs290256	JAGN1	trans	parietal	SCAN
rs290256	GADD45G	cis	cerebellum	SCAN

Chromatin state (count:51 , 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	chr9:93643400-93651800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:93643400-93652800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:93643600-93665400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:93646200-93664800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:93646800-93657000	Weak transcription	NHEK	skin
11	chr9:93647200-93663400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr9:93647400-93666600	Strong transcription	Primary B cells from cord blood	blood
13	chr9:93647600-93662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:93647600-93664800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:93647800-93654400	Strong transcription	Primary hematopoietic stem cells	blood
16	chr9:93647800-93662000	Strong transcription	Fetal Thymus	thymus
17	chr9:93648000-93662400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:93648200-93663200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:93648200-93665000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:93648600-93661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:93648800-93663200	Strong transcription	Thymus	Thymus
22	chr9:93649400-93652600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:93649800-93652800	Strong transcription	Spleen	Spleen
24	chr9:93650000-93652400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr9:93650000-93652600	Strong transcription	GM12878-XiMat	blood
26	chr9:93650000-93652800	Strong transcription	Fetal Intestine Large	intestine
27	chr9:93650000-93660800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr9:93650000-93661200	Strong transcription	Fetal Intestine Small	intestine
29	chr9:93650000-93661400	Strong transcription	Fetal Stomach	stomach
30	chr9:93650000-93662600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr9:93650600-93652200	Strong transcription	Liver	Liver
32	chr9:93650600-93652600	Strong transcription	Gastric	stomach
33	chr9:93650600-93652800	Strong transcription	Colonic Mucosa	Colon
34	chr9:93650600-93653200	Weak transcription	Brain Angular Gyrus	brain
35	chr9:93650800-93652400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr9:93650800-93653200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr9:93651000-93652400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr9:93651000-93652800	Strong transcription	Pancreas	Pancrea
39	chr9:93651200-93652200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:93651200-93652600	ZNF genes & repeats	Lung	lung
41	chr9:93651200-93653200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:93651400-93652800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:93651400-93652800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr9:93651400-93653000	Strong transcription	Esophagus	oesophagus
45	chr9:93651400-93653600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr9:93651600-93652000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:93651600-93652400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr9:93651600-93655800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr9:93651600-93657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:93651600-93661600	Weak transcription	Fetal Kidney	kidney

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