Variant report

Variant	rs10810397
Chromosome Location	chr9:15553591-15553592
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-3	chr9:15553289-15553604	NONHSAT130275

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10118359	0.84[EUR][1000 genomes]
rs10119975	0.80[EUR][1000 genomes]
rs10120726	0.84[ASN][1000 genomes]
rs10121393	0.83[EUR][1000 genomes]
rs10121591	0.85[EUR][1000 genomes]
rs10122339	0.81[EUR][1000 genomes]
rs10123042	0.83[EUR][1000 genomes]
rs10481557	0.81[CEU][hapmap]
rs10733295	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10738399	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10756673	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756674	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs10756687	0.81[CEU][hapmap]
rs10756688	0.81[CEU][hapmap]
rs10810399	0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs10810408	0.81[CEU][hapmap]
rs10810416	0.93[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810419	0.89[CEU][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810422	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10810424	0.84[EUR][1000 genomes]
rs10810426	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810427	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10810428	0.81[CEU][hapmap]
rs10810429	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10810430	0.81[EUR][1000 genomes]
rs10810438	0.89[CEU][hapmap];0.81[YRI][hapmap]
rs10962066	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs10962070	0.81[CEU][hapmap]
rs10962106	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10962121	0.81[EUR][1000 genomes]
rs10962123	0.81[EUR][1000 genomes]
rs10962125	0.81[EUR][1000 genomes]
rs10962126	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11792937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12004358	0.81[EUR][1000 genomes]
rs12341679	0.89[CEU][hapmap]
rs12349323	0.80[EUR][1000 genomes]
rs12352779	0.80[EUR][1000 genomes]
rs12377371	0.89[CEU][hapmap]
rs13301516	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1355171	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1396706	0.86[CEU][hapmap]
rs1533040	0.81[CEU][hapmap]
rs169342	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs183928	0.93[CEU][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1848582	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs192466	0.89[CEU][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs2055772	0.81[CEU][hapmap]
rs2175080	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2457265	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2457637	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2663300	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276432	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs276435	0.96[CEU][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs276436	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs276441	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs276443	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs276444	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs276447	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs276448	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276449	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs276453	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276454	0.85[CEU][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs276455	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2821545	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs28410434	0.81[EUR][1000 genomes]
rs3119699	0.85[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs3122702	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35057009	0.81[EUR][1000 genomes]
rs36086644	0.81[EUR][1000 genomes]
rs3955162	0.81[AMR][1000 genomes]
rs432452	0.93[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs433849	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs442549	0.93[CEU][hapmap];0.97[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs451878	0.92[CEU][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4740614	0.96[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4740615	0.81[CEU][hapmap]
rs4740619	0.81[CEU][hapmap]
rs4740624	0.81[CEU][hapmap]
rs4741516	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4741528	0.81[CEU][hapmap]
rs62573118	0.81[EUR][1000 genomes]
rs6474930	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6474944	0.81[CEU][hapmap]
rs6474946	0.84[EUR][1000 genomes]
rs6474951	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6474952	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7023275	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7030846	0.85[EUR][1000 genomes]
rs7031365	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7034484	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7034781	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs7035863	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7036285	0.81[EUR][1000 genomes]
rs7036674	0.83[CEU][hapmap]
rs7036875	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7037662	0.81[EUR][1000 genomes]
rs7037908	0.81[EUR][1000 genomes]
rs7042475	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7046351	0.84[EUR][1000 genomes]
rs7467156	0.89[CEU][hapmap];0.84[YRI][hapmap]
rs7467207	0.88[CEU][hapmap]
rs770524	0.93[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs7848511	0.85[EUR][1000 genomes]
rs7851056	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851323	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7860623	0.80[AMR][1000 genomes]
rs7860869	0.89[CEU][hapmap];0.81[YRI][hapmap]
rs7863088	0.81[CEU][hapmap]
rs7866629	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7873152	0.92[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7874533	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap]
rs7875367	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9407624	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs954663	0.89[CEU][hapmap]
rs9650684	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10810397	C9orf93	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15551800-15553800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr9:15551800-15553800	Active TSS	Brain Cingulate Gyrus	brain
3	chr9:15551800-15554200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:15551800-15554400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:15551800-15554400	Active TSS	Brain Angular Gyrus	brain
6	chr9:15551800-15554400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr9:15551800-15554400	Active TSS	Fetal Brain Female	brain
8	chr9:15551800-15554600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:15551800-15554600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr9:15552000-15553600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:15552000-15553600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:15552000-15553600	Active TSS	Primary T cells from cord blood	blood
13	chr9:15552000-15553600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr9:15552000-15553600	Active TSS	Fetal Muscle Leg	muscle
15	chr9:15552000-15553600	Active TSS	HSMM	muscle
16	chr9:15552000-15553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:15552000-15553800	Flanking Active TSS	Liver	Liver
18	chr9:15552000-15553800	Active TSS	Pancreas	Pancrea
19	chr9:15552000-15554000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr9:15552000-15554000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:15552000-15554000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:15552000-15554000	Active TSS	Brain Substantia Nigra	brain
23	chr9:15552000-15554000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr9:15552000-15554000	Active TSS	Rectal Smooth Muscle	rectum
25	chr9:15552000-15554000	Active TSS	Right Atrium	heart
26	chr9:15552000-15554000	Active TSS	Stomach Smooth Muscle	stomach
27	chr9:15552000-15554000	Active TSS	HSMMtube	muscle
28	chr9:15552000-15554200	Active TSS	Brain Hippocampus Middle	brain
29	chr9:15552000-15554400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:15552000-15554400	Active TSS	Thymus	Thymus
31	chr9:15552000-15554600	Active TSS	NHDF-Ad	bronchial
32	chr9:15552200-15553600	Active TSS	Colon Smooth Muscle	Colon
33	chr9:15552200-15553600	Active TSS	Fetal Heart	heart
34	chr9:15552200-15553600	Active TSS	Fetal Lung	lung
35	chr9:15552200-15553600	Active TSS	Left Ventricle	heart
36	chr9:15552200-15553600	Active TSS	Hela-S3	cervix
37	chr9:15552200-15553800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:15552200-15553800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:15552200-15553800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:15552200-15553800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:15552200-15553800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr9:15552200-15553800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:15552200-15553800	Active TSS	Esophagus	oesophagus
44	chr9:15552200-15553800	Active TSS	Gastric	stomach
45	chr9:15552200-15553800	Active TSS	Lung	lung
46	chr9:15552200-15553800	Active TSS	Ovary	ovary
47	chr9:15552200-15553800	Active TSS	Psoas Muscle	Psoas
48	chr9:15552200-15553800	Active TSS	Right Ventricle	heart
49	chr9:15552200-15553800	Active TSS	Stomach Mucosa	stomach
50	chr9:15552200-15554000	Active TSS	Aorta	Aorta

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