Variant report

Variant	rs10412931
Chromosome Location	chr19:40000075-40000076
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	chr19:39934123..39936292-chr19:39998837..40000591,2	K562	blood:
2	chr19:39922964..39925489-chr19:39998609..40000385,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EID2B-1	chr19:39998899-40000234	ucscGeneNc_uc002nwj_2

Variant related genes	Relation type
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10423537	0.89[EUR][1000 genomes]
rs10424217	0.82[EUR][1000 genomes]
rs1110627	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1130180	0.85[EUR][1000 genomes]
rs12609112	0.85[EUR][1000 genomes]
rs12978920	0.82[EUR][1000 genomes]
rs12983040	0.85[EUR][1000 genomes]
rs1529732	0.85[EUR][1000 genomes]
rs1560730	0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1865091	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1865092	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1932	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2009970	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2060270	0.86[EUR][1000 genomes]
rs2060271	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2060272	0.87[EUR][1000 genomes]
rs2116932	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2288933	0.93[ASW][hapmap];0.89[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2288934	0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2304219	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2304221	0.90[EUR][1000 genomes]
rs2353678	0.80[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs251855	0.85[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs251857	0.85[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs251859	0.85[CEU][hapmap]
rs28528765	0.86[EUR][1000 genomes]
rs28649498	0.85[EUR][1000 genomes]
rs31727	0.89[CEU][hapmap]
rs31728	0.88[CEU][hapmap]
rs34918990	0.89[EUR][1000 genomes]
rs35647910	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4390710	0.80[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4802026	0.82[EUR][1000 genomes]
rs4803237	0.85[EUR][1000 genomes]
rs4803240	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs4803241	0.84[EUR][1000 genomes]
rs4803242	0.85[EUR][1000 genomes]
rs4803245	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs4803246	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4803247	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4803250	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564577	0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs566130	0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs59007555	0.85[EUR][1000 genomes]
rs6508862	0.84[EUR][1000 genomes]
rs6508863	0.84[EUR][1000 genomes]
rs6508864	0.91[EUR][1000 genomes]
rs6508865	0.91[EUR][1000 genomes]
rs7251384	0.93[EUR][1000 genomes]
rs7251652	0.87[EUR][1000 genomes]
rs7255253	0.85[EUR][1000 genomes]
rs7257526	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73035416	0.86[EUR][1000 genomes]
rs73549933	0.86[EUR][1000 genomes]
rs8107194	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs8107647	0.86[EUR][1000 genomes]
rs8110134	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs8110716	0.84[EUR][1000 genomes]
rs8111260	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs878754	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv3374976	chr19:39998161-40023263	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10412931	GRIK5	cis	parietal	SCAN
rs10412931	WSB1	trans	multi-tissue	Pritchard
rs10412931	C19orf61	cis	cerebellum	SCAN
rs10412931	ENST00000301733	trans	multi-tissue	Pritchard
rs10412931	RPS16P7	cis	Liver	GTEx
rs10412931	B3GNT8	cis	parietal	SCAN
rs10412931	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs10412931	BCAM	cis	parietal	SCAN
rs10412931	WSB1	cis	Liver	GTEx
rs10412931	NUMBL	cis	parietal	SCAN
rs10412931	RPS16	cis	multi-tissue	Pritchard
rs10412931	RPS16	cis	lymphoblastoid	seeQTL
rs10412931	RPS16	cis	Liver	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39998400-40005400	Weak transcription	Right Atrium	heart
2	chr19:39999400-40005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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