Variant report

Variant	rs6478012
Chromosome Location	chr9:116246885-116246886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116244673..116249213-chr9:116254294..116256965,4	K562	blood:
2	chr9:116240264..116245059-chr9:116245363..116250466,7	MCF-7	breast:
3	chr9:116245555..116247785-chr9:116248959..116250962,2	MCF-7	breast:
4	chr9:116242234..116244423-chr9:116246310..116248311,2	MCF-7	breast:
5	chr9:116244969..116247316-chr9:116341587..116344549,2	MCF-7	breast:
6	chr9:116245986..116247736-chr9:116254544..116256250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10116799	0.83[GIH][hapmap]
rs10125960	0.81[CEU][hapmap]
rs10217237	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217341	0.83[GIH][hapmap]
rs10217750	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217756	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481640	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481676	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs10817496	1.00[ASN][1000 genomes]
rs10981794	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981803	0.83[GIH][hapmap]
rs10981808	0.81[CEU][hapmap]
rs10981817	0.81[CEU][hapmap]
rs10981819	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs10981828	0.83[GIH][hapmap]
rs10981840	1.00[ASN][1000 genomes]
rs10981841	1.00[ASN][1000 genomes]
rs10981843	1.00[ASN][1000 genomes]
rs10981844	1.00[ASN][1000 genomes]
rs10981845	1.00[ASN][1000 genomes]
rs10981846	1.00[ASN][1000 genomes]
rs10981847	1.00[ASN][1000 genomes]
rs10981850	1.00[ASN][1000 genomes]
rs12335991	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336719	0.81[CEU][hapmap]
rs12336983	1.00[ASN][1000 genomes]
rs12337340	0.81[CEU][hapmap]
rs12338221	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338697	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12339493	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12339501	0.83[GIH][hapmap]
rs12339617	0.81[CEU][hapmap]
rs12339851	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340996	0.81[CEU][hapmap]
rs12341332	0.81[CEU][hapmap]
rs12342508	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12342699	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12343129	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12343141	0.81[CEU][hapmap]
rs12343940	0.83[GIH][hapmap]
rs12344578	0.81[CEU][hapmap]
rs12344964	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345524	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs12346076	0.81[CEU][hapmap]
rs12346939	0.81[CEU][hapmap]
rs12347895	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs16907354	1.00[ASN][1000 genomes]
rs17187621	0.83[ASW][hapmap]
rs17766289	1.00[ASN][1000 genomes]
rs1890992	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs2050865	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs28709996	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36062487	1.00[ASN][1000 genomes]
rs3983381	0.81[CEU][hapmap]
rs41276817	1.00[ASN][1000 genomes]
rs41297197	1.00[ASN][1000 genomes]
rs4348575	1.00[ASN][1000 genomes]
rs4596719	0.81[CEU][hapmap]
rs4609260	1.00[ASN][1000 genomes]
rs511561	1.00[ASN][1000 genomes]
rs530456	1.00[ASN][1000 genomes]
rs538711	1.00[ASN][1000 genomes]
rs551960	1.00[ASN][1000 genomes]
rs55916010	1.00[ASN][1000 genomes]
rs56038206	1.00[ASN][1000 genomes]
rs57989349	1.00[ASN][1000 genomes]
rs586265	1.00[ASN][1000 genomes]
rs60302610	1.00[ASN][1000 genomes]
rs608290	1.00[ASN][1000 genomes]
rs611335	1.00[ASN][1000 genomes]
rs6478011	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs6478016	0.81[CEU][hapmap]
rs6478017	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478022	0.84[CEU][hapmap]
rs6478023	0.80[CEU][hapmap]
rs653971	1.00[ASN][1000 genomes]
rs664850	1.00[ASN][1000 genomes]
rs670719	1.00[ASN][1000 genomes]
rs7018783	0.81[CEU][hapmap]
rs7020623	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7021491	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021688	0.83[GIH][hapmap]
rs7023661	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7024445	0.81[CEU][hapmap]
rs7024996	0.81[CEU][hapmap]
rs7026656	0.81[CEU][hapmap]
rs7027024	0.80[CEU][hapmap]
rs7027340	0.81[CEU][hapmap]
rs7028327	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7033679	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037441	0.86[CEU][hapmap]
rs7040031	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7041833	0.81[CEU][hapmap]
rs7042695	0.80[CEU][hapmap]
rs7043140	0.81[CEU][hapmap]
rs7045347	0.80[CEU][hapmap]
rs7046202	0.81[CEU][hapmap]
rs7046427	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7047062	0.81[CEU][hapmap]
rs7048208	0.81[CEU][hapmap]
rs7048305	0.83[GIH][hapmap]
rs72761905	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761964	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761969	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761971	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761973	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761978	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72761995	1.00[ASN][1000 genomes]
rs7848203	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7851718	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7854197	0.81[CEU][hapmap]
rs7855325	0.83[GIH][hapmap]
rs7857943	0.81[CEU][hapmap]
rs7860673	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7861248	0.83[GIH][hapmap]
rs7863159	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7867203	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867353	0.81[CEU][hapmap]
rs7870227	0.81[CEU][hapmap]
rs7870265	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871186	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs7872283	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs9299215	0.81[CEU][hapmap]
rs9657641	0.81[CEU][hapmap]
rs9657659	0.81[CEU][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription 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	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6478012	C9orf91	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116227400-116263800	Weak transcription	Colonic Mucosa	Colon
2	chr9:116231600-116249800	Weak transcription	Hela-S3	cervix
3	chr9:116235000-116251200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:116236200-116252400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:116239200-116250200	Weak transcription	Psoas Muscle	Psoas
6	chr9:116240400-116254600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:116241200-116252800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:116241600-116247800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:116241800-116248800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:116241800-116252200	Strong transcription	Fetal Intestine Small	intestine
11	chr9:116242000-116248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:116242000-116254200	Weak transcription	Brain Germinal Matrix	brain
13	chr9:116242000-116254200	Weak transcription	Fetal Thymus	thymus
14	chr9:116242000-116255200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:116242000-116263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:116242000-116266200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:116242600-116254200	Weak transcription	Fetal Brain Female	brain
18	chr9:116242800-116247000	Enhancers	Pancreas	Pancrea
19	chr9:116243200-116247800	Weak transcription	Gastric	stomach
20	chr9:116244000-116247600	Weak transcription	A549	lung
21	chr9:116244000-116248000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:116244000-116249600	Weak transcription	Liver	Liver
23	chr9:116244800-116247000	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:116244800-116248400	Enhancers	Fetal Heart	heart
25	chr9:116245000-116247800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:116245000-116248800	Enhancers	Colon Smooth Muscle	Colon
27	chr9:116245000-116249000	Strong transcription	Fetal Intestine Large	intestine
28	chr9:116245200-116247000	Enhancers	Right Atrium	heart
29	chr9:116245400-116247000	Enhancers	Spleen	Spleen
30	chr9:116245600-116247000	Enhancers	Fetal Muscle Leg	muscle
31	chr9:116245600-116247200	Enhancers	Ovary	ovary
32	chr9:116245800-116247200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr9:116245800-116248000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:116245800-116248400	Enhancers	HUVEC	blood vessel
35	chr9:116245800-116248800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:116245800-116248800	Enhancers	Right Ventricle	heart
37	chr9:116245800-116248800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:116246000-116247000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:116246000-116247000	Enhancers	Brain Cingulate Gyrus	brain
40	chr9:116246000-116247000	Enhancers	Brain Hippocampus Middle	brain
41	chr9:116246000-116247000	Enhancers	Brain Substantia Nigra	brain
42	chr9:116246000-116247200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr9:116246000-116248600	Enhancers	NHLF	lung
44	chr9:116246200-116247000	Enhancers	Adipose Nuclei	Adipose
45	chr9:116246200-116247000	Enhancers	Brain Angular Gyrus	brain
46	chr9:116246200-116247000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:116246200-116247000	Enhancers	Small Intestine	intestine
48	chr9:116246200-116247200	Enhancers	Duodenum Mucosa	Duodenum
49	chr9:116246200-116247200	Enhancers	Fetal Lung	lung
50	chr9:116246400-116247000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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