Variant report

Variant	rs2501935
Chromosome Location	chr9:78989829-78989830
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10121699	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10869767	0.93[ASN][1000 genomes]
rs10869773	0.91[ASN][1000 genomes]
rs11144864	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11144865	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs11144866	0.82[ASN][1000 genomes]
rs11144871	0.94[ASN][1000 genomes]
rs11144880	0.92[ASN][1000 genomes]
rs12057052	0.85[ASN][1000 genomes]
rs12344941	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs13288968	0.86[ASN][1000 genomes]
rs13295433	0.91[ASN][1000 genomes]
rs13302654	1.00[ASN][1000 genomes]
rs1961995	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2002423	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2251604	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2377641	0.85[YRI][hapmap]
rs2490572	0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2490573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490574	0.85[ASN][1000 genomes]
rs2490576	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2490579	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2490583	0.82[ASN][1000 genomes]
rs2490584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2490586	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2501922	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501923	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501925	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501927	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501928	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501930	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2501932	0.88[ASN][1000 genomes]
rs2501933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501937	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501938	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501939	0.85[ASN][1000 genomes]
rs35837300	0.80[ASN][1000 genomes]
rs3739729	0.94[ASN][1000 genomes]
rs4372070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4745541	0.93[ASN][1000 genomes]
rs4745544	1.00[JPT][hapmap]
rs6560517	0.91[ASN][1000 genomes]
rs6560522	0.95[JPT][hapmap]
rs7035385	0.81[YRI][hapmap]
rs7038009	0.89[YRI][hapmap]
rs7847608	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7849239	0.91[ASN][1000 genomes]
rs785936	0.83[GIH][hapmap]
rs7861089	0.91[ASN][1000 genomes]

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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78980400-78990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:78986000-78990400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:78986800-78990400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr9:78986800-78990600	Enhancers	Liver	Liver
7	chr9:78986800-78990800	Enhancers	Fetal Intestine Large	intestine
8	chr9:78986800-78990800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr9:78986800-78991000	Enhancers	Fetal Stomach	stomach
10	chr9:78987000-78990000	Enhancers	Small Intestine	intestine
11	chr9:78987000-78990200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr9:78987000-78990600	Enhancers	Colon Smooth Muscle	Colon
13	chr9:78987000-78990600	Enhancers	Fetal Intestine Small	intestine
14	chr9:78987000-78990600	Enhancers	HepG2	liver
15	chr9:78987000-78991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:78987200-78990400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:78987200-78991200	Enhancers	Stomach Mucosa	stomach
18	chr9:78987400-78990000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:78988000-78990400	Enhancers	Fetal Muscle Leg	muscle
21	chr9:78988200-78990000	Weak transcription	HSMM	muscle
22	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
25	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
26	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
27	chr9:78988400-78990000	Weak transcription	Adipose Nuclei	Adipose
28	chr9:78988400-78990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
31	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:78988600-78994200	Weak transcription	HMEC	breast
34	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
40	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
41	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr9:78989000-78990000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:78989000-78990000	Enhancers	Colonic Mucosa	Colon
45	chr9:78989000-78990000	Weak transcription	Fetal Lung	lung
46	chr9:78989000-78990400	Enhancers	Pancreas	Pancrea
47	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
49	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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