Variant report

Variant	rs187744
Chromosome Location	chr2:180720392-180720393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10930884	1.00[CHB][hapmap]
rs10930885	1.00[CHB][hapmap]
rs1385970	1.00[CHB][hapmap]
rs1480701	1.00[ASN][1000 genomes]
rs1486232	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs165383	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165384	1.00[CHD][hapmap]
rs16867038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs16867040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs16867042	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17772985	1.00[CHB][hapmap]
rs17773184	1.00[CHB][hapmap]
rs17773255	1.00[CHB][hapmap]
rs17773308	1.00[CHB][hapmap]
rs17773504	1.00[CHB][hapmap]
rs17773667	1.00[CHB][hapmap]
rs17773899	1.00[CHB][hapmap]
rs17773927	1.00[CHB][hapmap]
rs17774379	1.00[CHB][hapmap]
rs17775571	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17775913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17775991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs17776109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17823821	1.00[CHB][hapmap]
rs17823881	1.00[CHB][hapmap]
rs17824301	1.00[CHB][hapmap]
rs17824564	1.00[CHB][hapmap]
rs17824691	1.00[CHB][hapmap]
rs17824733	1.00[CHB][hapmap]
rs17824871	1.00[CHB][hapmap]
rs17824913	1.00[CHB][hapmap]
rs17824948	1.00[CHB][hapmap]
rs17825041	1.00[CHB][hapmap]
rs17825125	1.00[CHB][hapmap]
rs17825317	1.00[CHB][hapmap]
rs17825747	1.00[CHB][hapmap]
rs17831917	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2126424	1.00[CHB][hapmap]
rs2169484	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2367798	1.00[CHB][hapmap]
rs2367800	1.00[CHB][hapmap]
rs259814	1.00[CHD][hapmap]
rs34879134	1.00[ASN][1000 genomes]
rs55781930	1.00[ASN][1000 genomes]
rs59351466	1.00[ASN][1000 genomes]
rs59429726	1.00[ASN][1000 genomes]
rs59777414	1.00[ASN][1000 genomes]
rs6433805	1.00[CHB][hapmap]
rs6433806	1.00[CHB][hapmap]
rs6433808	1.00[CHB][hapmap]
rs6718670	1.00[CHB][hapmap]
rs6727665	1.00[CHB][hapmap]
rs6738348	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756801	1.00[ASN][1000 genomes]
rs73973764	1.00[ASN][1000 genomes]
rs7557892	1.00[CHB][hapmap]
rs7570042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7574741	1.00[CHB][hapmap]
rs7581371	1.00[CHB][hapmap]
rs7602719	1.00[CHB][hapmap]

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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs187744	PDE1A	cis	parietal	SCAN
rs187744	NEUROD1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180706800-180724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180718200-180720600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:180718200-180723600	Weak transcription	Liver	Liver
4	chr2:180719800-180720400	Enhancers	Fetal Lung	lung
5	chr2:180719800-180720800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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