Variant report

Variant	rs12006522
Chromosome Location	chr9:100652711-100652712
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100651715..100653516-chr9:100817722..100819986,2	K562	blood:
2	chr9:100472419..100473515-chr9:100652192..100652909,5	K562	blood:
3	chr9:100472975..100473600-chr9:100651604..100652809,3	MCF-7	breast:
4	chr9:100651977..100652889-chr9:100663107..100663913,3	MCF-7	breast:
5	chr9:100648546..100652838-chr9:100654754..100658082,3	K562	blood:
6	chr9:100652340..100652880-chr9:100663048..100663789,2	K562	blood:
7	chr9:100464367..100467056-chr9:100650913..100653289,2	K562	blood:
8	chr9:100652278..100654064-chr9:100658870..100661083,2	MCF-7	breast:
9	chr9:100639207..100640135-chr9:100652414..100652928,2	MCF-7	breast:
10	chr9:100645728..100648046-chr9:100651565..100653285,2	K562	blood:
11	chr9:100511988..100512975-chr9:100652311..100652871,4	MCF-7	breast:
12	chr9:100633555..100634377-chr9:100652125..100652748,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1007506	0.80[CHB][hapmap]
rs10113884	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10115216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117642	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10119760	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119853	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10120412	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122541	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123699	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10512255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512256	1.00[YRI][hapmap]
rs1059003	1.00[YRI][hapmap]
rs10739526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759975	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759981	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10760011	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10818175	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818213	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818241	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10984079	0.83[ASN][1000 genomes]
rs10984103	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984134	0.83[ASN][1000 genomes]
rs10984156	0.83[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984218	0.87[ASN][1000 genomes]
rs10984222	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10984235	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984311	0.88[CHB][hapmap]
rs10984377	1.00[YRI][hapmap]
rs10984424	0.82[CHB][hapmap]
rs10984516	1.00[YRI][hapmap]
rs10984532	1.00[YRI][hapmap]
rs10984545	1.00[YRI][hapmap]
rs12004762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343182	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347191	0.81[EUR][1000 genomes]
rs12375612	1.00[YRI][hapmap]
rs12550872	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286291	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13287360	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13299924	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1348387	1.00[YRI][hapmap]
rs1443434	0.89[CEU][hapmap]
rs1443435	0.89[CEU][hapmap]
rs1443436	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687621	1.00[YRI][hapmap]
rs1867278	0.85[CEU][hapmap]
rs1947015	1.00[YRI][hapmap]
rs1955143	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1955144	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955145	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120262	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2120264	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417575	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417576	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28417086	0.87[ASN][1000 genomes]
rs28697997	0.87[ASN][1000 genomes]
rs28703314	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3021525	0.85[ASN][1000 genomes]
rs35324451	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3758249	0.89[CEU][hapmap]
rs3758250	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3758251	0.89[CEU][hapmap]
rs3808893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap]
rs3824495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255258	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4460498	0.81[EUR][1000 genomes]
rs4743139	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743142	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478445	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6478469	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478471	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022148	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027221	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7032114	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037175	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044121	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044799	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753537	0.91[ASN][1000 genomes]
rs7851498	1.00[YRI][hapmap]
rs7854948	1.00[YRI][hapmap]
rs7860144	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866436	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868534	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs894673	0.89[CEU][hapmap]
rs907577	0.89[CEU][hapmap]
rs907581	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs925487	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9299258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775370	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs993501	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12006522	C9orf156	cis	Frontal Cortex	GTEx
rs12006522	C9orf156	cis	Temporal Cortex	GTEx
rs12006522	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100637600-100658000	Weak transcription	Gastric	stomach
2	chr9:100637800-100652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:100651800-100652800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr9:100651800-100653000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:100651800-100653000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr9:100652000-100653000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr9:100652200-100652800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:100652200-100652800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:100652200-100652800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr9:100652200-100652800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:100652200-100652800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr9:100652200-100652800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:100652200-100652800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:100652200-100653000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:100652200-100653000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr9:100652200-100653000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:100652200-100653000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:100652400-100652800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr9:100652400-100653000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr9:100652400-100654400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:100652400-100657400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:100652600-100652800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr9:100652600-100652800	Enhancers	Primary T cells from cord blood	blood
24	chr9:100652600-100652800	Enhancers	Fetal Lung	lung
25	chr9:100652600-100653000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:100652600-100653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:100652600-100653400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:100652600-100654000	Enhancers	Adipose Nuclei	Adipose
29	chr9:100652600-100654600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:100652600-100659600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:100652600-100662400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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