Variant report

Variant	rs1099909
Chromosome Location	chr9:102905448-102905449
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10116798	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10117150	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1014651	0.83[ASN][1000 genomes]
rs1014652	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739796	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10760720	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819737	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819739	0.86[ASN][1000 genomes]
rs10989009	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1099910	0.83[ASN][1000 genomes]
rs12336751	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13301295	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1338119	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415926	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1535667	0.83[ASN][1000 genomes]
rs1572607	0.84[ASN][1000 genomes]
rs1891334	0.83[AMR][1000 genomes]
rs1999877	0.83[ASN][1000 genomes]
rs2209082	0.80[ASN][1000 genomes]
rs2476439	0.86[ASN][1000 genomes]
rs2476441	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2476442	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2485745	0.81[AMR][1000 genomes]
rs2485746	0.81[AMR][1000 genomes]
rs2491095	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2761053	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2761056	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2787361	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2787363	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787364	0.81[ASN][1000 genomes]
rs2787365	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2787366	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2787369	0.82[AMR][1000 genomes]
rs2787381	0.82[AMR][1000 genomes]
rs2787383	0.81[AMR][1000 genomes]
rs2787385	0.82[AMR][1000 genomes]
rs2787391	0.85[AMR][1000 genomes]
rs2787394	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2787395	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2787397	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2806681	0.81[ASN][1000 genomes]
rs2806682	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2806683	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2806684	0.81[ASN][1000 genomes]
rs2806692	0.81[AMR][1000 genomes]
rs2806693	0.81[AMR][1000 genomes]
rs2806694	0.82[AMR][1000 genomes]
rs4743384	0.81[AMR][1000 genomes]
rs6479001	0.83[AMR][1000 genomes]
rs6479002	0.83[AMR][1000 genomes]
rs7047092	0.81[ASN][1000 genomes]
rs7846794	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7847213	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7856844	0.86[ASN][1000 genomes]
rs7859492	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7861003	0.86[AMR][1000 genomes]
rs846751	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs846752	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846753	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs846756	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs846758	0.83[AFR][1000 genomes]
rs846761	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs846765	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs846766	0.83[ASN][1000 genomes]
rs846768	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846769	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846770	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860171	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs863668	0.86[ASN][1000 genomes]
rs9299337	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9408995	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9409325	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9695692	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9886877	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102874200-102912600	Weak transcription	Osteobl	bone
2	chr9:102874200-102937600	Weak transcription	Aorta	Aorta
3	chr9:102879800-102935000	Weak transcription	Ovary	ovary
4	chr9:102883000-102937600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:102883800-102928400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:102885200-102932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:102886000-102931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:102887800-102922200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:102889000-102907000	Weak transcription	K562	blood
10	chr9:102889200-102936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:102889600-102934600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:102891800-102935200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:102892200-102909200	Weak transcription	Fetal Stomach	stomach
14	chr9:102893000-102934600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:102893800-102936200	Weak transcription	Primary B cells from cord blood	blood
16	chr9:102895200-102920600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:102902400-102907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:102903400-102907800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:102904000-102906600	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
20	chr9:102904200-102905800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
21	chr9:102904200-102906000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
22	chr9:102904400-102906600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
23	chr9:102904800-102905600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:102904800-102906800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:102905000-102906200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr9:102905000-102908800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:102905200-102905600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:102905200-102905800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:102905200-102906000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:102905200-102906400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:102905200-102908800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:102905200-102908800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:102905400-102907000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links