Variant report

Variant	rs11723550
Chromosome Location	chr4:120289961-120289962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10002914	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10003742	0.83[ASN][1000 genomes]
rs10004114	0.80[ASN][1000 genomes]
rs10013652	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10015883	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10020256	0.83[AFR][1000 genomes]
rs10021601	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10026436	0.85[AFR][1000 genomes]
rs10517834	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11098505	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11098506	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11722183	0.83[AFR][1000 genomes]
rs11737400	0.84[EUR][1000 genomes]
rs12374244	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12374245	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12374352	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12499602	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12501602	0.80[AFR][1000 genomes]
rs12510451	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12510487	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12513310	0.81[AFR][1000 genomes]
rs13104572	0.84[AFR][1000 genomes]
rs13105020	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13125526	0.81[ASN][1000 genomes]
rs13132082	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13149954	0.84[EUR][1000 genomes]
rs1814815	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2017058	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28439855	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28501434	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28580295	0.82[EUR][1000 genomes]
rs28668103	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4643791	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62320740	0.84[EUR][1000 genomes]
rs67281037	0.83[AFR][1000 genomes]
rs6824111	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6824169	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6846966	0.80[ASN][1000 genomes]
rs6847586	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6847778	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6848081	0.85[AFR][1000 genomes]
rs6848580	0.83[AFR][1000 genomes]
rs6857892	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72676059	0.80[AFR][1000 genomes]
rs7677068	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9637624	0.81[EUR][1000 genomes]
rs9991221	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9995136	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking 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 target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking 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	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11723550	RP11-33B1.1	cis	Whole Blood	GTEx
rs11723550	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11723550	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120269600-120293000	Weak transcription	Fetal Heart	heart
2	chr4:120282600-120290000	Weak transcription	HepG2	liver
3	chr4:120285400-120290000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:120285400-120291600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:120285800-120291000	Weak transcription	Primary T cells from cord blood	blood
6	chr4:120286000-120291200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:120288400-120291400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:120288400-120291400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:120288400-120291600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:120288600-120291200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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