Variant report

Variant	rs7682931
Chromosome Location	chr4:153060217-153060218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10030518	0.96[ASN][1000 genomes]
rs11099843	0.96[ASN][1000 genomes]
rs11721407	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721782	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11726930	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727188	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11727862	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732677	0.95[CEU][hapmap];0.83[MEX][hapmap]
rs11733393	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733971	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736628	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737156	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112841	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131134	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276520	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17361258	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17361391	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs1991223	0.87[MEX][hapmap]
rs2406622	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406625	0.96[ASN][1000 genomes]
rs28531716	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2897478	1.00[ASN][1000 genomes]
rs34069606	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34276148	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34771630	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34909306	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296212	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4557238	0.96[ASN][1000 genomes]
rs56780740	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61226564	0.96[ASN][1000 genomes]
rs6535839	0.96[ASN][1000 genomes]
rs6535840	0.96[ASN][1000 genomes]
rs66476112	0.87[AMR][1000 genomes]
rs6823091	0.96[ASN][1000 genomes]
rs6833264	1.00[ASN][1000 genomes]
rs6837375	0.96[ASN][1000 genomes]
rs6843947	0.96[ASN][1000 genomes]
rs6848307	0.86[ASN][1000 genomes]
rs6858062	0.95[CEU][hapmap]
rs72736219	0.86[AMR][1000 genomes]
rs7662581	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671283	0.92[ASN][1000 genomes]
rs7674458	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675252	1.00[ASN][1000 genomes]
rs7675481	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv880774	chr4:153035743-153121818	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7682931	DCLK2	cis	cerebellum	SCAN
rs7682931	MAB21L2	cis	parietal	SCAN
rs7682931	RP11-18H21.1	cis	Whole Blood	GTEx
rs7682931	SMAD1	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153055400-153060400	Enhancers	Fetal Thymus	thymus
2	chr4:153056200-153060400	Enhancers	Thymus	Thymus
3	chr4:153059000-153060400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:153059200-153060400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:153059200-153060400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr4:153059200-153060400	Enhancers	HSMMtube	muscle
7	chr4:153059600-153060400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr4:153060000-153060400	Active TSS	Spleen	Spleen
9	chr4:153060200-153060600	Enhancers	Dnd41	blood

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