Variant report

Variant	rs2544920
Chromosome Location	chr5:100141374-100141375
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100139903..100141553-chr5:100144664..100147138,2	K562	blood:
2	chr5:100140257..100142972-chr5:100150394..100152547,2	K562	blood:

Variant related genes	Relation type
ENSG00000221263	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10044903	0.85[ASN][1000 genomes]
rs10052474	0.89[ASN][1000 genomes]
rs10057237	0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10058901	0.83[EUR][1000 genomes]
rs10059953	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10060686	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10072493	0.84[ASN][1000 genomes]
rs10072498	0.84[ASN][1000 genomes]
rs10075853	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078251	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10078934	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10214216	0.80[EUR][1000 genomes]
rs10463771	0.87[ASN][1000 genomes]
rs10463772	0.87[ASN][1000 genomes]
rs10477661	0.84[EUR][1000 genomes]
rs10478598	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478599	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478649	0.84[EUR][1000 genomes]
rs11241752	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs11241755	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs11584	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738152	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs11741369	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742480	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs11742504	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs11745097	0.81[ASN][1000 genomes]
rs11748306	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12153670	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs12332145	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12332642	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12719316	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13357545	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13358325	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs13358607	0.81[ASN][1000 genomes]
rs13360613	0.81[ASN][1000 genomes]
rs13436424	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13857	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423380	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1428439	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs149895	0.83[ASN][1000 genomes]
rs1541676	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs1559058	0.86[ASN][1000 genomes]
rs1559059	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs157043	0.83[ASN][1000 genomes]
rs17723545	0.85[ASN][1000 genomes]
rs17724185	0.87[ASN][1000 genomes]
rs17725452	0.83[ASN][1000 genomes]
rs17726244	0.84[EUR][1000 genomes]
rs17778837	0.81[ASN][1000 genomes]
rs17780091	0.86[ASN][1000 genomes]
rs17780273	0.87[ASN][1000 genomes]
rs17780471	0.85[ASN][1000 genomes]
rs17780525	0.87[ASN][1000 genomes]
rs17782250	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1820150	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2059845	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs2544913	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2548256	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2548257	0.81[EUR][1000 genomes]
rs2548261	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548262	0.83[ASN][1000 genomes]
rs2548264	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548265	0.82[EUR][1000 genomes]
rs2548274	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548276	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548278	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548280	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2561520	0.83[ASN][1000 genomes]
rs2725116	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2725124	0.96[CEU][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276457	0.83[ASN][1000 genomes]
rs276460	0.81[ASN][1000 genomes]
rs276462	0.83[ASN][1000 genomes]
rs276465	0.82[ASN][1000 genomes]
rs277869	0.82[ASN][1000 genomes]
rs277871	0.84[ASN][1000 genomes]
rs277872	0.84[ASN][1000 genomes]
rs278494	0.83[ASN][1000 genomes]
rs278495	0.83[ASN][1000 genomes]
rs278496	0.83[ASN][1000 genomes]
rs278497	0.83[ASN][1000 genomes]
rs278498	0.83[ASN][1000 genomes]
rs278499	0.83[ASN][1000 genomes]
rs278501	0.83[ASN][1000 genomes]
rs278502	0.83[ASN][1000 genomes]
rs278503	0.83[ASN][1000 genomes]
rs278504	0.83[ASN][1000 genomes]
rs28413976	0.83[ASN][1000 genomes]
rs3756350	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs3756351	0.81[EUR][1000 genomes]
rs3776155	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776167	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs3776170	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs3776171	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs3776176	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs3822366	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs3843478	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3846626	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846627	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs3857365	0.86[ASN][1000 genomes]
rs3909452	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs3909453	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4702991	0.87[ASN][1000 genomes]
rs4703115	0.81[ASN][1000 genomes]
rs4703116	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4703117	0.81[ASN][1000 genomes]
rs4703118	0.81[ASN][1000 genomes]
rs4703119	0.81[ASN][1000 genomes]
rs4703126	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4703127	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs4703128	0.86[ASN][1000 genomes]
rs4703133	0.86[EUR][1000 genomes]
rs55817847	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55849330	0.87[ASN][1000 genomes]
rs57055845	0.81[ASN][1000 genomes]
rs59030588	0.83[EUR][1000 genomes]
rs59490571	0.84[ASN][1000 genomes]
rs60853907	0.84[EUR][1000 genomes]
rs6864315	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6883673	0.84[ASN][1000 genomes]
rs6886392	0.81[ASN][1000 genomes]
rs726971	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs72776700	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72778607	0.85[ASN][1000 genomes]
rs72778613	0.87[ASN][1000 genomes]
rs72778620	0.87[ASN][1000 genomes]
rs72778635	0.83[ASN][1000 genomes]
rs7447673	0.87[ASN][1000 genomes]
rs7703643	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7710701	0.81[ASN][1000 genomes]
rs7736024	0.82[ASN][1000 genomes]
rs7737721	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9327319	0.85[ASN][1000 genomes]
rs9327323	0.84[ASN][1000 genomes]
rs9327327	0.87[ASN][1000 genomes]
rs966257	0.92[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2544920	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100138400-100142400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:100138400-100142600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:100138800-100143800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr5:100139000-100146400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:100139400-100154400	Weak transcription	Fetal Lung	lung
6	chr5:100139400-100155400	Weak transcription	Placenta	Placenta
7	chr5:100139600-100142400	Weak transcription	Dnd41	blood
8	chr5:100139600-100143400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:100139600-100144400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:100139600-100149200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:100140200-100147000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:100140800-100147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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