Variant report

Variant	rs16954999
Chromosome Location	chr18:44610718-44610719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12953864	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12960378	0.86[GIH][hapmap]
rs12968552	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13381713	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1434529	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16954921	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1836259	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2289036	0.88[ASW][hapmap]
rs2289133	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317324	0.92[CEU][hapmap]
rs2461247	0.81[GIH][hapmap]
rs2571002	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2571004	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2571005	0.92[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2571006	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2571007	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2571008	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2571009	0.83[YRI][hapmap]
rs2571010	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2571014	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2571016	0.86[GIH][hapmap]
rs2571017	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576052	0.92[CEU][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2576057	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2576058	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2576060	0.86[GIH][hapmap]
rs2635049	0.86[GIH][hapmap]
rs2635051	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635052	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635054	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635056	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2668758	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2668759	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2668761	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2668762	0.87[EUR][1000 genomes]
rs2668763	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668784	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2684819	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2684833	0.92[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2684851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28718304	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932126	0.81[GIH][hapmap]
rs36095873	0.80[EUR][1000 genomes]
rs3816125	0.81[GIH][hapmap]
rs4986228	0.82[TSI][hapmap]
rs55730206	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7239323	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7242978	0.83[GIH][hapmap]
rs7504798	0.86[GIH][hapmap]
rs8085634	0.92[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9951617	0.80[EUR][1000 genomes]
rs9953157	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9956809	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9960264	0.81[GIH][hapmap]
rs9961383	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962436	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909611	chr18:44560875-44614090	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1067278	chr18:44564162-44629283	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16954999	IER3IP1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44579800-44630200	Weak transcription	Right Ventricle	heart
2	chr18:44586800-44629600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:44587200-44630600	Weak transcription	Brain Anterior Caudate	brain
4	chr18:44587600-44629400	Weak transcription	Liver	Liver
5	chr18:44588200-44621600	Weak transcription	Left Ventricle	heart
6	chr18:44598200-44630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:44602200-44610800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr18:44602200-44630000	Weak transcription	Fetal Muscle Leg	muscle
9	chr18:44602400-44611600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:44603400-44614200	Weak transcription	Brain Substantia Nigra	brain
11	chr18:44603800-44614400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:44603800-44630000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr18:44604000-44613000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr18:44604000-44630200	Weak transcription	Adipose Nuclei	Adipose
15	chr18:44604000-44630600	Weak transcription	Brain Angular Gyrus	brain
16	chr18:44604800-44630800	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:44605400-44630400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr18:44610000-44611000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr18:44610200-44611200	Weak transcription	Psoas Muscle	Psoas
22	chr18:44610600-44610800	Weak transcription	Fetal Muscle Trunk	muscle

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