Variant report

Variant	rs2273998
Chromosome Location	chr9:8524854-8524855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10117042	0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs10120190	0.85[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10123125	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123138	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10124867	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10511499	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10758978	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758979	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758980	0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815883	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10815896	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10815898	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10815900	0.85[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10815905	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815906	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815907	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10815908	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10977146	0.83[JPT][hapmap]
rs10977169	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10977170	0.82[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10977181	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10977189	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10977195	0.80[YRI][hapmap]
rs10977196	0.83[AMR][1000 genomes]
rs12340211	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341045	0.81[ASN][1000 genomes]
rs12341078	0.82[JPT][hapmap]
rs12344975	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12350641	0.95[LWK][hapmap];0.80[AFR][1000 genomes]
rs12683581	0.83[JPT][hapmap]
rs12686431	0.83[JPT][hapmap]
rs17650044	0.83[JPT][hapmap]
rs1998513	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1998515	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs3763652	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763653	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477313	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2273998	C1orf212	trans	brain	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
3	chr9:8492400-8528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
5	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
6	chr9:8509400-8528600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:8509800-8532800	Weak transcription	Brain Angular Gyrus	brain
8	chr9:8518000-8528600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:8518200-8526400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:8518400-8526000	Weak transcription	Ovary	ovary
11	chr9:8518400-8533800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:8518400-8534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:8518400-8555200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:8519800-8531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:8520000-8531200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:8521200-8525000	Strong transcription	Fetal Lung	lung
17	chr9:8521800-8526200	Weak transcription	Dnd41	blood
18	chr9:8522000-8528200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:8522000-8528600	Weak transcription	Brain Germinal Matrix	brain
20	chr9:8522200-8531400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:8522400-8529200	Weak transcription	Brain Anterior Caudate	brain
22	chr9:8522400-8530800	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:8522400-8531600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:8522600-8527200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:8523800-8525400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:8524000-8525000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:8524200-8531600	Weak transcription	Brain Substantia Nigra	brain
28	chr9:8524400-8525800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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