Variant report

Variant	rs10739099
Chromosome Location	chr9:6427481-6427482
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6411987..6416661-chr9:6426661..6431000,5	K562	blood:
2	chr9:6413061..6414947-chr9:6424688..6427649,3	MCF-7	breast:
3	chr9:6417024..6418829-chr9:6426585..6429333,3	K562	blood:
4	chr9:6425850..6427575-chr9:6427743..6430006,2	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10115362	0.87[ASN][1000 genomes]
rs10115883	0.88[JPT][hapmap]
rs10122116	0.95[JPT][hapmap]
rs10124572	0.89[ASN][1000 genomes]
rs10733529	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739100	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739102	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758783	0.86[ASN][1000 genomes]
rs10758784	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10758785	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758786	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758787	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758791	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10758792	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815428	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10815435	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10975579	0.91[ASN][1000 genomes]
rs10975582	0.93[ASN][1000 genomes]
rs10975583	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10975585	0.94[ASN][1000 genomes]
rs10975595	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10975605	0.88[JPT][hapmap]
rs1156747	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11790625	0.91[ASN][1000 genomes]
rs11791651	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11795355	0.89[JPT][hapmap]
rs12346455	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12347573	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12351293	0.89[ASN][1000 genomes]
rs12376117	0.86[ASN][1000 genomes]
rs13283381	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs13291472	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs13292799	0.92[ASN][1000 genomes]
rs13298500	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs13440427	0.86[ASN][1000 genomes]
rs1381035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381036	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381037	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16924328	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs16924562	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs16924591	0.88[ASN][1000 genomes]
rs16924624	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs16924626	0.95[JPT][hapmap]
rs16924631	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs16924634	0.83[JPT][hapmap]
rs1824537	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870696	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1903419	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2065074	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065075	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169283	0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2169286	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2381444	0.91[ASN][1000 genomes]
rs3739654	0.82[CEU][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs380674	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs394137	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs414107	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4380997	0.84[ASN][1000 genomes]
rs4384035	0.89[ASN][1000 genomes]
rs452135	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4556138	0.86[ASN][1000 genomes]
rs4740844	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740845	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742199	0.98[ASN][1000 genomes]
rs4742201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742204	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs504698	0.88[ASN][1000 genomes]
rs530722	0.86[ASN][1000 genomes]
rs55960819	0.89[ASN][1000 genomes]
rs56218473	0.94[ASN][1000 genomes]
rs56396114	0.89[ASN][1000 genomes]
rs56939673	0.91[ASN][1000 genomes]
rs569866	0.86[ASN][1000 genomes]
rs6477086	0.84[ASN][1000 genomes]
rs6477087	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs67852216	0.87[ASN][1000 genomes]
rs7027302	0.89[ASN][1000 genomes]
rs7029772	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7033940	0.89[ASN][1000 genomes]
rs7034328	0.80[ASN][1000 genomes]
rs73401679	0.87[ASN][1000 genomes]
rs7852539	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs7853059	0.87[ASN][1000 genomes]
rs7853834	0.87[ASN][1000 genomes]
rs7857628	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7860427	0.87[ASN][1000 genomes]
rs7860966	0.93[ASN][1000 genomes]
rs7861073	0.93[ASN][1000 genomes]
rs7861559	0.93[ASN][1000 genomes]
rs7865955	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7871134	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7873756	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10739099	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
2	chr9:6414600-6449000	Weak transcription	Gastric	stomach
3	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
5	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
6	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:6415600-6430000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
11	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:6416400-6429800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:6416400-6430000	Weak transcription	Spleen	Spleen
15	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
16	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:6417400-6434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:6417600-6430600	Weak transcription	HSMM	muscle
19	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:6417800-6428600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:6417800-6428800	Weak transcription	K562	blood
22	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
23	chr9:6418000-6438200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:6418200-6428600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr9:6418800-6430600	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:6419000-6428600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:6419000-6437000	Weak transcription	Fetal Brain Male	brain
28	chr9:6419200-6430600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:6419200-6433800	Weak transcription	Brain Substantia Nigra	brain
30	chr9:6419200-6437800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:6419400-6428400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:6419400-6428600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:6419400-6432200	Weak transcription	Brain Anterior Caudate	brain
34	chr9:6419400-6437400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:6419600-6427800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:6420000-6429800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:6420400-6430600	Weak transcription	Ovary	ovary
38	chr9:6420800-6428800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:6420800-6430400	Weak transcription	Small Intestine	intestine
40	chr9:6421000-6429200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:6421200-6427600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr9:6421200-6428200	Strong transcription	HepG2	liver
43	chr9:6421400-6449400	Weak transcription	Liver	Liver
44	chr9:6421800-6430200	Weak transcription	Left Ventricle	heart
45	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
46	chr9:6422400-6428200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:6422400-6428600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:6422600-6427800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:6422800-6427600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:6422800-6427800	Weak transcription	Fetal Kidney	kidney

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