Variant report

Variant	rs9884518
Chromosome Location	chr4:173739355-173739356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10000607	0.80[AMR][1000 genomes]
rs10012267	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10022095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10025284	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10029310	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10031191	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10033472	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10213357	1.00[JPT][hapmap]
rs1097574	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11132960	1.00[JPT][hapmap]
rs11734921	1.00[JPT][hapmap]
rs12108242	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12512892	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12645987	1.00[JPT][hapmap]
rs1370576	1.00[JPT][hapmap]
rs1370577	1.00[JPT][hapmap]
rs1455119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1540474	1.00[JPT][hapmap]
rs1561307	1.00[JPT][hapmap]
rs1658515	1.00[JPT][hapmap]
rs17058762	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17058765	1.00[JPT][hapmap]
rs17058894	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17058922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058946	1.00[CEU][hapmap]
rs17235632	1.00[JPT][hapmap]
rs1821862	1.00[JPT][hapmap]
rs1870436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2009141	1.00[CEU][hapmap]
rs2083136	1.00[JPT][hapmap]
rs2118443	1.00[JPT][hapmap]
rs2164822	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2164823	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2164824	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2164826	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2332544	1.00[JPT][hapmap]
rs28479395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484578	0.85[AFR][1000 genomes]
rs28637185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28681326	0.85[AFR][1000 genomes]
rs4100737	1.00[JPT][hapmap]
rs4423855	1.00[JPT][hapmap]
rs4572851	1.00[JPT][hapmap]
rs6553647	1.00[JPT][hapmap]
rs6811397	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6826006	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6827725	1.00[CEU][hapmap]
rs6839897	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6841156	1.00[JPT][hapmap]
rs6844959	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6848466	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap]
rs716647	1.00[JPT][hapmap]
rs7671554	1.00[CEU][hapmap]
rs7674050	1.00[JPT][hapmap]
rs7686162	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7694956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7699455	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs837209	1.00[CEU][hapmap]
rs837213	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9312528	1.00[JPT][hapmap]
rs9312533	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9884494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9992243	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9993208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs9994145	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9995075	1.00[JPT][hapmap]

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	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3327952	chr4:173591786-173805861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9884518	TCL1A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173715000-173740200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:173731400-173747400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:173737200-173742400	Weak transcription	Stomach Mucosa	stomach
4	chr4:173737400-173742000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:173737400-173742000	Weak transcription	Fetal Intestine Large	intestine
6	chr4:173737400-173742200	Weak transcription	Fetal Intestine Small	intestine

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