Variant report

Variant	rs2406625
Chromosome Location	chr4:153056573-153056574
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10030518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099843	0.91[ASN][1000 genomes]
rs11721407	0.91[ASN][1000 genomes]
rs11721782	0.91[ASN][1000 genomes]
rs11726930	0.91[ASN][1000 genomes]
rs11727862	0.91[ASN][1000 genomes]
rs11733393	0.85[ASN][1000 genomes]
rs11733971	0.91[ASN][1000 genomes]
rs11736628	0.96[ASN][1000 genomes]
rs11737156	0.96[ASN][1000 genomes]
rs13112841	0.96[ASN][1000 genomes]
rs13131134	0.96[ASN][1000 genomes]
rs13147317	0.88[EUR][1000 genomes]
rs2406622	0.96[ASN][1000 genomes]
rs2897478	0.96[ASN][1000 genomes]
rs34069606	0.91[ASN][1000 genomes]
rs34276148	0.96[ASN][1000 genomes]
rs34909306	0.96[ASN][1000 genomes]
rs35296212	0.91[ASN][1000 genomes]
rs4557238	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56780740	0.89[ASN][1000 genomes]
rs61226564	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535836	0.80[EUR][1000 genomes]
rs6535837	0.80[EUR][1000 genomes]
rs6535839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535840	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823091	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833264	0.96[ASN][1000 genomes]
rs6837375	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843300	0.87[EUR][1000 genomes]
rs6843947	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848307	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6858503	0.82[CEU][hapmap]
rs747110	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7662581	0.96[ASN][1000 genomes]
rs7668917	0.80[EUR][1000 genomes]
rs7671283	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7674458	0.96[ASN][1000 genomes]
rs7675252	0.96[ASN][1000 genomes]
rs7675481	0.96[ASN][1000 genomes]
rs7682931	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2406625	RP11-18H21.1	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153048200-153059200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:153050200-153058600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:153055400-153060400	Enhancers	Fetal Thymus	thymus
4	chr4:153056200-153058600	Enhancers	Dnd41	blood
5	chr4:153056200-153060400	Enhancers	Thymus	Thymus
6	chr4:153056400-153056600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:153056400-153059400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links