Variant report

Variant	rs17492872
Chromosome Location	chr2:98828918-98828919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98822445..98824064-chr2:98827178..98830158,2	K562	blood:

Variant related genes	Relation type
ENSG00000231635	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13428410	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs17426979	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17427034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17427096	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17427272	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4132465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4132466	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154930	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154931	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154932	0.93[AMR][1000 genomes]
rs62154933	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62154937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156669	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62156674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62156675	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62156684	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62156685	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62156687	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17492872	SNORD50A	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98827600-98829800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:98827600-98830200	Enhancers	Fetal Stomach	stomach
3	chr2:98828000-98829000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:98828000-98829000	Enhancers	Rectal Smooth Muscle	rectum
5	chr2:98828000-98829800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:98828000-98830000	Enhancers	Colon Smooth Muscle	Colon
7	chr2:98828400-98829400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:98828400-98829600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:98828400-98829600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:98828400-98829800	Enhancers	Fetal Brain Male	brain
11	chr2:98828400-98830000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:98828600-98829000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:98828600-98829000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:98828600-98829400	Enhancers	Fetal Brain Female	brain
15	chr2:98828600-98829800	Enhancers	Brain Germinal Matrix	brain
16	chr2:98828800-98829000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:98828800-98829200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:98828800-98829200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:98828800-98829600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:98828800-98829600	Enhancers	Fetal Kidney	kidney

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