Variant report

Variant	rs16924562
Chromosome Location	chr9:6450551-6450552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10115362	0.81[ASN][1000 genomes]
rs10115883	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10122116	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10124572	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10125914	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10733529	0.87[ASN][1000 genomes]
rs10739098	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10739099	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739100	0.89[ASN][1000 genomes]
rs10739102	0.86[ASN][1000 genomes]
rs10758783	0.83[ASN][1000 genomes]
rs10758784	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10758785	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10758786	0.85[ASN][1000 genomes]
rs10758787	0.85[ASN][1000 genomes]
rs10758788	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10758789	0.81[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10758790	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10758791	0.89[ASN][1000 genomes]
rs10758792	0.90[ASN][1000 genomes]
rs10815428	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10815435	0.90[ASN][1000 genomes]
rs10975579	0.80[ASN][1000 genomes]
rs10975582	0.82[ASN][1000 genomes]
rs10975583	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10975585	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10975595	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10975603	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10975605	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1156747	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11790625	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11791651	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11795228	0.82[AMR][1000 genomes]
rs11795355	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12346455	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12347573	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12351293	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12376117	0.82[ASN][1000 genomes]
rs13283381	0.94[CHB][hapmap]
rs13289925	0.82[ASN][1000 genomes]
rs13291472	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13292799	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13298500	0.86[CHB][hapmap]
rs13440427	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381035	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1381036	0.88[ASN][1000 genomes]
rs1381037	0.87[ASN][1000 genomes]
rs16924328	0.85[JPT][hapmap]
rs16924591	0.93[ASN][1000 genomes]
rs16924624	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16924626	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16924631	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16924634	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes]
rs1824537	0.87[ASN][1000 genomes]
rs1870696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1903419	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2065074	0.85[ASN][1000 genomes]
rs2065075	0.85[ASN][1000 genomes]
rs2169283	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2169286	0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2381444	0.80[ASN][1000 genomes]
rs33962342	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs3739654	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs380674	0.89[ASN][1000 genomes]
rs3818705	0.82[CHB][hapmap]
rs394137	0.83[ASN][1000 genomes]
rs414107	0.86[ASN][1000 genomes]
rs4380997	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4384035	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4463484	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs452135	0.85[ASN][1000 genomes]
rs4556138	0.89[ASN][1000 genomes]
rs4740844	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4740845	0.86[ASN][1000 genomes]
rs4742199	0.86[ASN][1000 genomes]
rs4742201	0.81[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4742202	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4742204	0.88[ASN][1000 genomes]
rs504698	0.93[ASN][1000 genomes]
rs530722	0.91[ASN][1000 genomes]
rs55960819	0.94[ASN][1000 genomes]
rs56218473	0.91[ASN][1000 genomes]
rs56396114	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56939673	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs569866	0.91[ASN][1000 genomes]
rs6477086	0.87[ASN][1000 genomes]
rs6477087	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs66509816	0.96[EUR][1000 genomes]
rs67852216	0.81[ASN][1000 genomes]
rs7027302	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7029772	0.94[CHB][hapmap]
rs7033570	0.84[ASN][1000 genomes]
rs7033940	0.93[ASN][1000 genomes]
rs7034328	0.83[ASN][1000 genomes]
rs73399080	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73401025	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73401679	0.92[ASN][1000 genomes]
rs7852539	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7853059	0.92[ASN][1000 genomes]
rs7853834	0.92[ASN][1000 genomes]
rs7857628	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7860427	0.81[ASN][1000 genomes]
rs7860966	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7861073	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7861559	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865955	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7871134	0.90[ASN][1000 genomes]
rs7873756	0.83[ASN][1000 genomes]
rs7876000	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16924562	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
2	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
3	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
4	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
5	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:6435000-6460400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:6435000-6463800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6438600-6460000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:6441600-6454600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:6442200-6455800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:6443000-6461600	Weak transcription	HepG2	liver
15	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:6443800-6450600	Weak transcription	Osteobl	bone
17	chr9:6445000-6461200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:6445600-6451200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr9:6446200-6451400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr9:6446200-6460600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:6446400-6452200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:6446600-6451200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr9:6446600-6455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:6446800-6452200	Weak transcription	Fetal Stomach	stomach
25	chr9:6446800-6463400	Weak transcription	Fetal Intestine Large	intestine
26	chr9:6446800-6468200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:6447000-6455200	Weak transcription	Fetal Intestine Small	intestine
28	chr9:6447200-6450800	Genic enhancers	HUVEC	blood vessel
29	chr9:6447200-6451000	Enhancers	Brain Anterior Caudate	brain
30	chr9:6447200-6451200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr9:6447200-6463400	Weak transcription	Lung	lung
32	chr9:6447400-6450600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr9:6447400-6450800	Enhancers	Brain Hippocampus Middle	brain
34	chr9:6447400-6451200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:6447400-6451400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr9:6447800-6450600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr9:6448200-6454000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:6448600-6451000	Genic enhancers	Primary T cells from cord blood	blood
39	chr9:6448800-6450800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr9:6448800-6451000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:6448800-6451200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr9:6448800-6451200	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr9:6449000-6451000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:6449000-6451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:6449000-6451000	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:6449000-6451000	Enhancers	Brain Substantia Nigra	brain
47	chr9:6449000-6451000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:6449200-6450600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:6449200-6450800	Genic enhancers	NHDF-Ad	bronchial
50	chr9:6449200-6451000	Enhancers	Brain Inferior Temporal Lobe	brain

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