Variant report

Variant	rs10738393
Chromosome Location	chr9:15426572-15426573
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15420915..15423147-chr9:15426389..15428949,2	K562	blood:
2	chr9:15420595..15424773-chr9:15424796..15433036,11	MCF-7	breast:
3	chr9:15420090..15425077-chr9:15425243..15430966,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10081655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10115540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10117968	0.94[CHB][hapmap];0.89[MKK][hapmap]
rs1033056	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs1046388	0.88[AFR][1000 genomes]
rs10733292	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10738392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10738395	0.84[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[ASN][1000 genomes]
rs10738397	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10738398	0.83[AFR][1000 genomes]
rs10756664	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10756666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10962036	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962039	0.81[AFR][1000 genomes]
rs1123038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12093	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs12339417	0.83[LWK][hapmap]
rs1397214	0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs1397215	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1567452	0.88[ASN][1000 genomes]
rs1976599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2175259	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2382530	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2665504	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2737829	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2737835	0.80[JPT][hapmap]
rs2737842	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2777950	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4510953	0.82[AMR][1000 genomes]
rs4741500	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4741501	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4741502	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4741504	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4741505	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4741506	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4741507	0.89[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4741508	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6474915	0.88[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap]
rs6474916	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6474918	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6474923	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7021042	0.89[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7026910	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7026970	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7037580	0.86[AFR][1000 genomes]
rs7042165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7046713	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7862428	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs907075	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs907076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9650682	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9650683	0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	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
rs10738393	C9orf150	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15423600-15434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:15423600-15439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:15424000-15427600	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr9:15424000-15430200	Weak transcription	Small Intestine	intestine
5	chr9:15424000-15431000	Weak transcription	Psoas Muscle	Psoas
6	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:15424200-15426600	Enhancers	Fetal Heart	heart
9	chr9:15424200-15426600	Strong transcription	Fetal Muscle Leg	muscle
10	chr9:15424200-15426800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:15424400-15426600	Genic enhancers	Dnd41	blood
12	chr9:15424600-15426600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:15424600-15426800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:15424600-15427000	Genic enhancers	Fetal Lung	lung
15	chr9:15424600-15427800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr9:15424600-15428400	Strong transcription	Fetal Thymus	thymus
17	chr9:15424600-15430400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:15424800-15426600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:15424800-15426600	Genic enhancers	Brain Hippocampus Middle	brain
20	chr9:15424800-15426600	Strong transcription	Brain Substantia Nigra	brain
21	chr9:15424800-15426600	Genic enhancers	Colon Smooth Muscle	Colon
22	chr9:15424800-15426600	Genic enhancers	Duodenum Mucosa	Duodenum
23	chr9:15424800-15426600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
24	chr9:15424800-15426600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr9:15424800-15426600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr9:15424800-15426800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr9:15424800-15427000	Genic enhancers	HepG2	liver
28	chr9:15424800-15427400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:15424800-15427400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr9:15424800-15427800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr9:15424800-15427800	Strong transcription	Placenta	Placenta
32	chr9:15424800-15428000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:15424800-15428400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr9:15424800-15428800	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr9:15424800-15430600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:15425000-15426600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:15425000-15426600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr9:15425000-15426600	Strong transcription	Brain Anterior Caudate	brain
39	chr9:15425000-15426600	Genic enhancers	Brain Germinal Matrix	brain
40	chr9:15425000-15426600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
41	chr9:15425000-15426600	Genic enhancers	Fetal Intestine Small	intestine
42	chr9:15425000-15426800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:15425000-15426800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:15425000-15426800	Genic enhancers	Fetal Brain Male	brain
45	chr9:15425000-15426800	Genic enhancers	NHDF-Ad	bronchial
46	chr9:15425000-15426800	Strong transcription	Osteobl	bone
47	chr9:15425000-15427000	Genic enhancers	Fetal Brain Female	brain
48	chr9:15425000-15427000	Strong transcription	NHEK	skin
49	chr9:15425000-15427200	Strong transcription	NH-A	brain
50	chr9:15425000-15427400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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