Variant report

Variant	rs10503409
Chromosome Location	chr8:10669654-10669655
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10503410	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1106740	0.84[EUR][1000 genomes]
rs11776368	1.00[CHD][hapmap]
rs11995539	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11998382	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12155811	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12156345	1.00[CHD][hapmap]
rs12375394	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12750	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1549792	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1549793	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17712981	0.81[EUR][1000 genomes]
rs17718772	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs17720365	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17721089	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs17774331	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17774398	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs17774627	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs17776404	0.95[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17776427	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17776497	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17776622	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17776946	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2005310	0.84[EUR][1000 genomes]
rs2409654	1.00[CHD][hapmap]
rs2409655	1.00[CHD][hapmap]
rs4240671	1.00[CHD][hapmap]
rs4310166	1.00[CHD][hapmap]
rs4326350	1.00[CHD][hapmap]
rs4841458	1.00[CHD][hapmap]
rs55637012	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55848210	0.92[EUR][1000 genomes]
rs56023918	0.84[EUR][1000 genomes]
rs56046029	0.92[EUR][1000 genomes]
rs56109041	0.84[EUR][1000 genomes]
rs56122299	0.84[EUR][1000 genomes]
rs57348261	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58193873	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6984391	0.84[EUR][1000 genomes]
rs7002757	0.84[EUR][1000 genomes]
rs7009920	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs714370	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73200740	0.81[EUR][1000 genomes]
rs73200742	0.82[EUR][1000 genomes]
rs73208756	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73208757	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73208762	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73208766	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73208769	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73208773	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73208775	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73208778	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73208781	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208782	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73208785	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73208789	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208790	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208791	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208793	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208794	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73208795	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73209913	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73209918	0.91[EUR][1000 genomes]
rs73209921	0.91[EUR][1000 genomes]
rs73209922	0.87[EUR][1000 genomes]
rs7817252	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7817654	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7826036	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7827063	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7838335	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs7845731	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs891558	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs891559	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9650658	0.90[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs9650659	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519768	chr8:10600254-10691993	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv831232	chr8:10606053-10774948	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv519376	chr8:10611708-10691993	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv429860	chr8:10615990-10685890	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019754	chr8:10617908-10700140	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv539471	chr8:10617908-10700140	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1031726	chr8:10627742-10749369	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10503409	CTSB	cis	cerebellum	SCAN
rs10503409	DEFB136	cis	parietal	SCAN
rs10503409	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10620000-10669800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr8:10640200-10669800	Weak transcription	Aorta	Aorta
3	chr8:10645000-10670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:10647000-10674400	Weak transcription	Right Ventricle	heart
5	chr8:10647000-10681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr8:10647200-10673600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:10647800-10669800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:10648200-10669800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr8:10648200-10683400	Weak transcription	Brain Angular Gyrus	brain
10	chr8:10650000-10676200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:10650600-10671200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr8:10657200-10670000	Weak transcription	Lung	lung
13	chr8:10657400-10681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:10657400-10685800	Weak transcription	Psoas Muscle	Psoas
15	chr8:10657600-10670000	Weak transcription	Gastric	stomach
16	chr8:10657600-10674200	Weak transcription	Pancreas	Pancrea
17	chr8:10657600-10674600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:10657600-10674600	Weak transcription	Esophagus	oesophagus
19	chr8:10657600-10674600	Weak transcription	Left Ventricle	heart
20	chr8:10657600-10681800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr8:10657800-10673000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:10657800-10673200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:10657800-10674400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:10657800-10674600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr8:10657800-10680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:10657800-10680600	Weak transcription	HSMMtube	muscle
27	chr8:10658400-10673000	Weak transcription	Liver	Liver
28	chr8:10658400-10676000	Weak transcription	HepG2	liver
29	chr8:10658600-10673400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr8:10658600-10676000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:10659400-10673400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:10659400-10676000	Weak transcription	NHLF	lung
33	chr8:10659600-10682400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:10659800-10669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:10660000-10679200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:10660200-10673400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:10660400-10670600	Weak transcription	Osteobl	bone
38	chr8:10660400-10677000	Weak transcription	NHDF-Ad	bronchial
39	chr8:10662000-10673400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:10662200-10671400	Weak transcription	Brain Substantia Nigra	brain
41	chr8:10662600-10674400	Weak transcription	Brain Anterior Caudate	brain
42	chr8:10662600-10676000	Weak transcription	Brain Germinal Matrix	brain
43	chr8:10662800-10674400	Weak transcription	Brain Hippocampus Middle	brain
44	chr8:10663000-10681200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr8:10663000-10681400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr8:10663000-10696200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr8:10663200-10673400	Weak transcription	HMEC	breast
48	chr8:10664000-10670600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr8:10664400-10670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr8:10664600-10670000	Weak transcription	HUVEC	blood vessel

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