Variant report

Variant	rs2341438
Chromosome Location	chr12:122921339-122921340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122908536..122910322-chr12:122920778..122923252,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10161184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10161488	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10744218	0.92[EUR][1000 genomes]
rs10744242	0.81[CHB][hapmap]
rs10773090	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs10773108	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773162	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773230	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs10846714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10846852	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10846871	0.97[ASN][1000 genomes]
rs10846899	0.84[ASN][1000 genomes]
rs10846912	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs10846968	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs11057514	0.81[EUR][1000 genomes]
rs11057522	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs11057686	0.84[EUR][1000 genomes]
rs11057813	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057819	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11058178	0.80[ASN][1000 genomes]
rs11058272	0.89[EUR][1000 genomes]
rs1129167	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs11503023	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11610303	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap]
rs11830957	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314537	0.92[EUR][1000 genomes]
rs12812332	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs12817342	0.86[CHB][hapmap]
rs12818177	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12819355	0.82[ASN][1000 genomes]
rs12828876	0.82[EUR][1000 genomes]
rs12829449	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1392142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532579	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1553178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4356269	0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4758657	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4758658	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758660	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs4758664	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758665	0.81[EUR][1000 genomes]
rs4758692	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758693	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758695	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61021925	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6416295	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs6488947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6489014	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs6489051	0.81[CHB][hapmap]
rs6489056	0.87[GIH][hapmap]
rs7134381	0.81[CHB][hapmap]
rs7296680	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7298839	0.81[CHB][hapmap]
rs7305360	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311573	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7313121	0.88[EUR][1000 genomes]
rs7313284	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs7953204	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7955241	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7955513	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7959550	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961258	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7964981	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7970007	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7972832	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973480	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974160	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7975492	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7978119	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7978636	0.81[EUR][1000 genomes]
rs868181	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs9788228	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2341438	DYNLL1	cis	parietal	SCAN
rs2341438	CCDC62	cis	cerebellum	SCAN
rs2341438	NME2P1	cis	cerebellum	SCAN
rs2341438	DIABLO	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122908400-122922000	Weak transcription	Right Atrium	heart
2	chr12:122908800-122921800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:122916400-122921800	Weak transcription	Brain Angular Gyrus	brain
4	chr12:122916600-122921400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:122916800-122921400	Weak transcription	Placenta	Placenta
6	chr12:122917400-122921400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:122920600-122921800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:122921200-122922000	Enhancers	Cortex derived primary cultured neurospheres	brain

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