Variant report

Variant	rs1250027
Chromosome Location	chr9:117860951-117860952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10982535	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1250019	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1250021	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1250022	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1250026	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1273108	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1330355	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1330356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1511	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1755639	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1755646	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757106	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs1757107	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1819419	0.94[EUR][1000 genomes]
rs1929395	0.95[JPT][hapmap]
rs2183701	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274836	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2480930	0.83[ASN][1000 genomes]
rs2480932	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2480933	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2482080	0.83[JPT][hapmap]
rs2989518	0.83[JPT][hapmap]
rs3789867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs944227	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
2	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:117849600-117864600	Weak transcription	HMEC	breast
4	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:117853400-117861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:117855200-117861000	Weak transcription	NH-A	brain
8	chr9:117857200-117861000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:117857400-117867400	Weak transcription	NHLF	lung
10	chr9:117857600-117866000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:117857600-117866800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:117858800-117861200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:117858800-117863000	Enhancers	Colon Smooth Muscle	Colon
14	chr9:117858800-117865600	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:117859000-117861000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr9:117859000-117861800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:117859400-117862800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:117859400-117865800	Weak transcription	NHEK	skin
19	chr9:117859600-117863600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:117859600-117865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:117860000-117861400	Enhancers	Liver	Liver
22	chr9:117860000-117863000	Enhancers	Fetal Lung	lung
23	chr9:117860000-117864600	Enhancers	Stomach Smooth Muscle	stomach
24	chr9:117860200-117861000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:117860400-117861600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr9:117860400-117862600	Enhancers	Fetal Muscle Leg	muscle
27	chr9:117860400-117862600	Enhancers	Fetal Stomach	stomach
28	chr9:117860600-117861000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:117860600-117861000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:117860600-117861000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:117860600-117861000	Enhancers	Brain Anterior Caudate	brain
32	chr9:117860600-117861200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
33	chr9:117860600-117861800	Enhancers	Osteobl	bone
34	chr9:117860600-117862000	Enhancers	NHDF-Ad	bronchial
35	chr9:117860600-117862200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:117860600-117862600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:117860600-117862600	Enhancers	Fetal Kidney	kidney
38	chr9:117860800-117861000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr9:117860800-117861000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr9:117860800-117862800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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