Variant report

Variant	rs6542129
Chromosome Location	chr2:114128884-114128885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114127277..114131238-chr2:114131557..114134448,3	K562	blood:
2	chr2:113961213..113962188-chr2:114127876..114128919,5	K562	blood:
3	chr2:114012941..114014608-chr2:114128232..114129740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10179990	0.87[ASN][1000 genomes]
rs10181913	0.88[ASN][1000 genomes]
rs10182105	0.88[ASN][1000 genomes]
rs10194893	0.89[ASN][1000 genomes]
rs10194994	0.89[ASN][1000 genomes]
rs10196370	0.89[EUR][1000 genomes]
rs10197232	0.87[ASN][1000 genomes]
rs10204881	0.80[ASN][1000 genomes]
rs11123183	0.87[ASN][1000 genomes]
rs11123184	0.87[ASN][1000 genomes]
rs11123185	0.87[ASN][1000 genomes]
rs11680681	0.88[ASN][1000 genomes]
rs11687673	0.95[ASN][1000 genomes]
rs11694836	0.95[ASN][1000 genomes]
rs11887472	0.85[ASN][1000 genomes]
rs11895592	0.86[ASN][1000 genomes]
rs11902038	0.86[ASN][1000 genomes]
rs1210133	0.81[JPT][hapmap]
rs12711767	0.81[ASN][1000 genomes]
rs12711768	0.87[ASN][1000 genomes]
rs12711770	0.87[ASN][1000 genomes]
rs12711771	0.86[ASN][1000 genomes]
rs12711772	0.86[ASN][1000 genomes]
rs12995339	0.95[ASN][1000 genomes]
rs12998178	0.87[ASN][1000 genomes]
rs13000403	0.85[ASN][1000 genomes]
rs13023224	0.87[ASN][1000 genomes]
rs13024454	0.87[ASN][1000 genomes]
rs13026218	0.87[ASN][1000 genomes]
rs13392903	0.92[ASN][1000 genomes]
rs13395590	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13411628	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1823124	0.95[ASN][1000 genomes]
rs1867868	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1867869	0.86[ASN][1000 genomes]
rs1867870	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1968612	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968613	0.95[ASN][1000 genomes]
rs1968614	0.94[EUR][1000 genomes]
rs1968615	0.95[ASN][1000 genomes]
rs1968616	0.95[ASN][1000 genomes]
rs2034278	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2121374	0.95[ASN][1000 genomes]
rs2863961	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863962	0.92[ASN][1000 genomes]
rs2863963	0.93[ASN][1000 genomes]
rs28665757	0.87[ASN][1000 genomes]
rs3860399	0.95[ASN][1000 genomes]
rs4439970	0.95[ASN][1000 genomes]
rs4848333	0.95[ASN][1000 genomes]
rs4848334	0.95[ASN][1000 genomes]
rs4848335	0.95[ASN][1000 genomes]
rs4849205	0.88[ASN][1000 genomes]
rs4849209	0.85[ASN][1000 genomes]
rs4849211	0.87[ASN][1000 genomes]
rs4849212	0.86[ASN][1000 genomes]
rs4849213	0.86[ASN][1000 genomes]
rs4849214	0.85[ASN][1000 genomes]
rs58583672	0.95[ASN][1000 genomes]
rs6542130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542131	0.95[ASN][1000 genomes]
rs6542132	0.95[ASN][1000 genomes]
rs6704835	0.85[ASN][1000 genomes]
rs6706343	0.88[ASN][1000 genomes]
rs6711441	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717693	0.85[ASN][1000 genomes]
rs6724324	0.88[ASN][1000 genomes]
rs6728162	0.90[ASN][1000 genomes]
rs6735826	0.88[ASN][1000 genomes]
rs6745928	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748429	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749684	0.88[ASN][1000 genomes]
rs6750170	0.87[ASN][1000 genomes]
rs6755915	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6758869	0.84[EUR][1000 genomes]
rs7355765	0.85[ASN][1000 genomes]
rs7562990	0.85[ASN][1000 genomes]
rs7589946	0.85[ASN][1000 genomes]
rs7590492	0.85[ASN][1000 genomes]
rs7590707	0.82[ASN][1000 genomes]
rs7604877	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9653402	0.85[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	esv2757826	chr2:114074949-114253780	Enhancers Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759085	chr2:114074949-114428678	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1002255	chr2:114120037-114236620	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6542129	CBWD1///CBWD2///CBWD3///CBWD5///CBWD6///	N/A	lymphoblastoid	RTeQTL
rs6542129	ACTR3	cis	cerebellum	SCAN
rs6542129	SLC35F5	cis	parietal	SCAN
rs6542129	CBWD1	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114106800-114129800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:114126800-114131000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:114126800-114131200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:114127000-114131000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:114128400-114134200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:114128800-114147400	Weak transcription	A549	lung

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