Variant report

Variant	rs3824495
Chromosome Location	chr9:100663700-100663701
allele	A/C
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100472959..100473568-chr9:100663208..100663905,3	MCF-7	breast:
2	chr9:100472637..100473577-chr9:100662994..100663928,6	K562	blood:
3	chr9:100652340..100652880-chr9:100663048..100663789,2	K562	blood:
4	chr9:100662549..100664772-chr9:100675385..100677486,2	K562	blood:
5	chr9:100472598..100473541-chr9:100662995..100663732,5	MCF-7	breast:
6	chr9:100662130..100664191-chr9:100669480..100671871,2	MCF-7	breast:
7	chr9:100663583..100665725-chr9:100672529..100674637,2	K562	blood:
8	chr9:100661983..100664921-chr9:100679667..100682904,3	MCF-7	breast:
9	chr9:100459617..100461117-chr9:100662395..100665046,2	K562	blood:
10	chr9:100651977..100652889-chr9:100663107..100663913,3	MCF-7	breast:
11	chr9:100661987..100664493-chr9:100807895..100810404,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf156-1	chr9:100662493-100664123	XLOC_007801

No data

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1007506	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs10113884	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10115216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.98[TSI][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]
rs10117642	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119760	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119853	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10120412	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122541	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123699	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10512255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][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]
rs10512256	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1059003	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10739526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759975	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10760011	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818213	0.95[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	0.83[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	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984235	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[LWK][hapmap];1.00[YRI][hapmap]
rs10984532	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10984545	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12004762	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]
rs12006522	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]
rs12342417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343182	0.82[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	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286291	0.83[EUR][1000 genomes]
rs13287360	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299924	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1348387	1.00[YRI][hapmap]
rs1443434	0.89[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1443435	0.89[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs1443436	0.84[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687621	1.00[YRI][hapmap]
rs1867278	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1947015	1.00[YRI][hapmap]
rs1955143	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2120264	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417575	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417576	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28417086	0.87[ASN][1000 genomes]
rs28697997	0.87[ASN][1000 genomes]
rs28703314	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3021525	0.85[ASN][1000 genomes]
rs35324451	0.82[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap]
rs4255258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4460498	0.81[EUR][1000 genomes]
rs4743139	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743142	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478445	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6478469	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478471	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022148	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032086	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7032114	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034249	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034648	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][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]
rs7037175	0.84[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];0.93[AMR][1000 genomes];0.99[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];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042459	0.81[AMR][1000 genomes]
rs7044121	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044799	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048255	1.00[CHB][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]
rs72753537	0.91[ASN][1000 genomes]
rs7851498	1.00[YRI][hapmap]
rs7854948	1.00[YRI][hapmap]
rs7860144	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866436	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868534	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs894673	0.89[CEU][hapmap]
rs907577	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs907581	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs925487	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9299258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775370	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs993501	0.88[AMR][1000 genomes];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3824495	C9orf156	cis	cerebellum	SCAN
rs3824495	C9orf156	cis	Temporal Cortex	GTEx
rs3824495	Hs.43687	cis	multi-tissue	Pritchard
rs3824495	C9orf156	cis	Frontal Cortex	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100652800-100666600	Weak transcription	Fetal Lung	lung
2	chr9:100653000-100667000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:100654200-100666600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:100656000-100667600	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:100656000-100669400	Weak transcription	Brain Substantia Nigra	brain
6	chr9:100656200-100665600	Weak transcription	Dnd41	blood
7	chr9:100656200-100666800	Weak transcription	Brain Germinal Matrix	brain
8	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:100656400-100668400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:100656400-100669800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:100656400-100669800	Weak transcription	Fetal Brain Female	brain
12	chr9:100656600-100667000	Weak transcription	Brain Anterior Caudate	brain
13	chr9:100656800-100666800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:100656800-100668400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:100656800-100669400	Weak transcription	Left Ventricle	heart
16	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
17	chr9:100657000-100666600	Weak transcription	Placenta	Placenta
18	chr9:100657000-100669400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:100657000-100669400	Weak transcription	Right Ventricle	heart
20	chr9:100658000-100665000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:100658200-100664800	Weak transcription	Fetal Intestine Large	intestine
22	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:100658400-100669400	Weak transcription	Hela-S3	cervix
24	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:100658600-100665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:100658600-100666600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:100658600-100666800	Weak transcription	Pancreas	Pancrea
28	chr9:100658600-100667600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:100658600-100669400	Weak transcription	Gastric	stomach
30	chr9:100658600-100671600	Weak transcription	Ovary	ovary
31	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
32	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
33	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:100660000-100664200	Weak transcription	GM12878-XiMat	blood
35	chr9:100660200-100671200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:100660600-100665400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr9:100660600-100668400	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:100660800-100669400	Weak transcription	Aorta	Aorta
39	chr9:100661000-100666400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:100661200-100669800	Weak transcription	K562	blood
41	chr9:100662000-100665000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr9:100662000-100667400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr9:100662400-100663800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:100662400-100663800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:100662400-100663800	Strong transcription	Primary B cells from cord blood	blood
46	chr9:100662400-100666800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:100662400-100667200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr9:100662600-100666600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr9:100662600-100666800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr9:100662800-100665000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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