Variant report

Variant	rs2482077
Chromosome Location	chr9:117851672-117851673
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:29)

rs_ID	r²[population]
rs1061494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250019	0.87[GIH][hapmap]
rs1250023	0.80[JPT][hapmap]
rs1271449	0.96[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1272041	0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1330360	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360291	0.80[JPT][hapmap]
rs1511	0.87[GIH][hapmap];0.81[LWK][hapmap]
rs1617917	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755637	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757100	0.80[JPT][hapmap]
rs1757108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757109	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757110	1.00[ASN][1000 genomes]
rs1757111	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274836	0.87[GIH][hapmap]
rs2482078	0.80[JPT][hapmap]
rs2988578	0.80[JPT][hapmap]
rs2989519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789867	0.82[GIH][hapmap]
rs3789868	0.82[GIH][hapmap]
rs769331	0.82[GIH][hapmap]
rs944510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:117827200-117855200	Strong transcription	NH-A	brain
4	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
5	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:117847200-117856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:117848800-117852800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:117849000-117856400	Weak transcription	Brain Substantia Nigra	brain
9	chr9:117849200-117851800	Genic enhancers	NHDF-Ad	bronchial
10	chr9:117849400-117852000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:117849400-117852800	Weak transcription	Fetal Intestine Large	intestine
12	chr9:117849400-117853200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:117849400-117855400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:117849400-117855600	Weak transcription	Fetal Lung	lung
15	chr9:117849400-117856200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:117849400-117856800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
18	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:117849600-117852000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:117849600-117852400	Weak transcription	Fetal Stomach	stomach
21	chr9:117849600-117852600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:117849600-117856400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
24	chr9:117849600-117864600	Weak transcription	HMEC	breast
25	chr9:117849800-117852600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:117849800-117854600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:117850000-117852000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:117850400-117851800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:117850400-117853400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:117850600-117852400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:117850800-117852000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:117850800-117852400	Enhancers	Rectal Smooth Muscle	rectum
35	chr9:117850800-117857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:117851000-117852200	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:117851400-117852200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr9:117851400-117853400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:117851600-117852000	Weak transcription	NHLF	lung
41	chr9:117851600-117853400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:117851600-117853400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:117851600-117854400	Strong transcription	Osteobl	bone
44	chr9:117851600-117854600	Strong transcription	NHEK	skin
45	chr9:117851600-117855600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links