Variant report

Variant	rs12342417
Chromosome Location	chr9:100639065-100639066
allele	A/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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100617184..100619335-chr9:100637041..100639858,3	MCF-7	breast:
2	chr9:100639021..100641102-chr9:100655728..100657284,2	MCF-7	breast:
3	chr9:100636360..100639098-chr9:100684329..100685877,2	MCF-7	breast:
4	chr9:100637402..100640995-chr9:100649849..100652626,3	MCF-7	breast:
5	chr9:100632180..100634200-chr9:100639047..100640743,2	MCF-7	breast:
6	chr9:100563307..100565719-chr9:100637927..100639761,2	MCF-7	breast:
7	chr9:100637251..100639094-chr9:100643727..100646653,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf156-2	chr9:100638612-100639488	XLOC_007800

No data

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

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

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

rs_ID	r²[population]
rs10046805	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1007506	0.80[CHB][hapmap]
rs10113884	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10115216	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]
rs10117642	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10119760	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119853	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10120412	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122541	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123699	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10512255	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]
rs10739526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759975	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759981	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10818124	0.81[AMR][1000 genomes]
rs10818133	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10818175	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818213	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818241	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10984079	0.85[ASN][1000 genomes]
rs10984103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984134	0.85[ASN][1000 genomes]
rs10984156	0.85[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10984218	0.81[ASN][1000 genomes]
rs10984222	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10984230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984235	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10984253	0.95[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]
rs10984311	0.88[CHB][hapmap]
rs10984424	0.82[CHB][hapmap]
rs12004762	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]
rs12006522	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]
rs12341377	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343182	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347191	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12348304	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12348691	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12550872	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13286291	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13287360	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13299924	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443434	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1443435	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1443436	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867277	0.81[AMR][1000 genomes]
rs1867278	0.88[CEU][hapmap]
rs1867280	0.81[AMR][1000 genomes]
rs1955143	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1955144	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955145	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2120264	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs2401639	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2417575	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417576	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417086	0.81[ASN][1000 genomes]
rs28697997	0.81[ASN][1000 genomes]
rs28703314	0.85[EUR][1000 genomes]
rs3021525	0.83[ASN][1000 genomes]
rs3021526	0.81[AMR][1000 genomes]
rs35324451	0.80[EUR][1000 genomes]
rs3758248	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3758249	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3758250	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs3758251	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3808893	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]
rs3808895	0.90[CHB][hapmap]
rs3824495	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]
rs4255258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4460498	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743139	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743142	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478437	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6478445	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6478469	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478471	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022148	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027221	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7031386	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]
rs7032086	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032114	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7034249	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7034336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034648	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036589	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]
rs7037175	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037324	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]
rs7038998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7044121	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7044799	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72753537	0.81[ASN][1000 genomes]
rs7851552	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7860144	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866436	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7868534	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894673	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs907577	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs907581	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs925487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9299258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9775370	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs993501	0.90[AMR][1000 genomes];0.97[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
rs12342417	C9orf156	cis	Temporal Cortex	GTEx
rs12342417	Hs.43687	cis	multi-tissue	Pritchard
rs12342417	C9orf156	cis	Frontal Cortex	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100631800-100639400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:100635800-100640400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:100636000-100640400	Enhancers	HMEC	breast
6	chr9:100636600-100639600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:100637600-100658000	Weak transcription	Gastric	stomach
8	chr9:100637800-100639800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:100637800-100652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:100638000-100642800	Weak transcription	Right Atrium	heart
11	chr9:100638200-100640000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:100638400-100639200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:100638400-100640000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr9:100638400-100640200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:100638400-100640200	Enhancers	NHDF-Ad	bronchial
16	chr9:100638600-100639200	Enhancers	HSMM	muscle
17	chr9:100638600-100639200	Enhancers	Osteobl	bone
18	chr9:100638600-100639400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:100638600-100640000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:100638600-100640000	Enhancers	HSMMtube	muscle
21	chr9:100638600-100640200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:100638600-100640200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr9:100638600-100640600	Enhancers	NHLF	lung
24	chr9:100638800-100639400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
25	chr9:100638800-100639600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr9:100638800-100639800	Flanking Active TSS	NH-A	brain
27	chr9:100638800-100640000	Flanking Active TSS	Hela-S3	cervix
28	chr9:100638800-100640000	Flanking Active TSS	NHEK	skin
29	chr9:100639000-100639200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:100639000-100639200	Enhancers	Esophagus	oesophagus
31	chr9:100639000-100639400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:100639000-100639400	Bivalent Enhancer	Placenta	Placenta
33	chr9:100639000-100639600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr9:100639000-100639800	Enhancers	Brain Hippocampus Middle	brain
35	chr9:100639000-100639800	Active TSS	A549	lung
36	chr9:100639000-100639800	Enhancers	HepG2	liver
37	chr9:100639000-100640000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:100639000-100640200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:100639000-100640600	Enhancers	Adipose Nuclei	Adipose

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