Variant report

Variant	rs2988578
Chromosome Location	chr9:117860295-117860296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1061494	0.80[JPT][hapmap]
rs1250023	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1250026	0.93[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1271449	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs1272041	0.80[JPT][hapmap]
rs1273108	0.92[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1330349	0.92[CEU][hapmap]
rs1330350	0.93[CEU][hapmap]
rs1330360	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1360291	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1617917	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs1755638	0.81[JPT][hapmap]
rs1755640	0.87[JPT][hapmap]
rs1757096	0.80[JPT][hapmap]
rs1757100	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757108	0.83[JPT][hapmap]
rs1888220	0.81[JPT][hapmap]
rs1929395	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs2480931	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2482077	0.80[JPT][hapmap]
rs2482078	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2482080	0.93[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2989518	0.93[CEU][hapmap]
rs2989519	0.80[JPT][hapmap]
rs2992147	0.80[JPT][hapmap]
rs944510	0.80[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	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

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
2	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
3	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:117849600-117864600	Weak transcription	HMEC	breast
5	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:117853400-117861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:117854000-117860600	Weak transcription	NHDF-Ad	bronchial
11	chr9:117854400-117860600	Weak transcription	Osteobl	bone
12	chr9:117855200-117861000	Weak transcription	NH-A	brain
13	chr9:117856800-117860400	Weak transcription	Fetal Stomach	stomach
14	chr9:117857200-117860400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:117857200-117861000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:117857400-117867400	Weak transcription	NHLF	lung
17	chr9:117857600-117866000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:117857600-117866800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:117858800-117861200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:117858800-117863000	Enhancers	Colon Smooth Muscle	Colon
21	chr9:117858800-117865600	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:117859000-117861000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr9:117859000-117861800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:117859400-117862800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:117859400-117865800	Weak transcription	NHEK	skin
26	chr9:117859600-117860600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:117859600-117863600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:117859600-117865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:117859800-117860600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:117860000-117860400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:117860000-117861400	Enhancers	Liver	Liver
32	chr9:117860000-117863000	Enhancers	Fetal Lung	lung
33	chr9:117860000-117864600	Enhancers	Stomach Smooth Muscle	stomach
34	chr9:117860200-117860600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:117860200-117861000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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