Variant report

Variant	rs17501094
Chromosome Location	chr2:98950106-98950107
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1010387	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes]
rs11684812	1.00[AFR][1000 genomes]
rs11684899	1.00[AFR][1000 genomes]
rs11691306	0.82[CEU][hapmap];1.00[AFR][1000 genomes]
rs13402201	0.90[AMR][1000 genomes]
rs13430738	0.83[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs17427608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17427825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17428745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17428990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17429379	0.97[EUR][1000 genomes]
rs17500406	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4564827	0.83[CEU][hapmap]
rs62155312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62155317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62155347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62155354	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62155355	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62155358	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156265	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156266	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156268	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156269	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156346	1.00[AFR][1000 genomes]
rs62156681	0.90[AMR][1000 genomes]
rs62156686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs62156724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62156744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62157892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62157901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62157907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62157908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62157916	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72817785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72817792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72817793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72819903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72819917	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72819919	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72819921	0.97[EUR][1000 genomes]
rs72819925	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72819927	0.86[AMR][1000 genomes];0.97[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17501094	NMS	cis	cerebellum	SCAN
rs17501094	SEMA4C	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98946800-98950400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:98948400-98951400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98948800-98952800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:98949000-98950200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:98949000-98953200	Enhancers	Brain Germinal Matrix	brain
6	chr2:98949200-98950800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:98949200-98952000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:98949400-98950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:98949400-98951200	Enhancers	NHDF-Ad	bronchial
10	chr2:98949400-98951600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:98949600-98950200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:98949600-98950400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:98949600-98950600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:98949600-98951200	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:98949600-98952200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr2:98950000-98950200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr2:98950000-98950200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:98950000-98950200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr2:98950000-98950200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
20	chr2:98950000-98950200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr2:98950000-98950200	Enhancers	HSMM	muscle
22	chr2:98950000-98950200	Enhancers	NH-A	brain
23	chr2:98950000-98950400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr2:98950000-98950400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr2:98950000-98950800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:98950000-98950800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr2:98950000-98950800	Flanking Active TSS	Osteobl	bone
28	chr2:98950000-98951000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:98950000-98951000	Enhancers	Fetal Brain Female	brain
30	chr2:98950000-98951000	Enhancers	HSMMtube	muscle
31	chr2:98950000-98951200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr2:98950000-98951800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:98950000-98952000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:98950000-98952000	Enhancers	NHLF	lung

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