Variant report

Variant	rs161199
Chromosome Location	chr3:21528920-21528921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11129010	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs11708571	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs11716643	1.00[ASN][1000 genomes]
rs12491476	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs12494223	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096493	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs151280	0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs151281	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163480	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs163481	0.85[EUR][1000 genomes]
rs190171	0.86[EUR][1000 genomes]
rs2126822	1.00[YRI][hapmap]
rs233144	0.85[EUR][1000 genomes]
rs233165	0.84[MEX][hapmap];0.86[TSI][hapmap]
rs233167	0.82[EUR][1000 genomes]
rs233168	0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs340097	0.84[EUR][1000 genomes]
rs34356086	1.00[ASN][1000 genomes]
rs35612116	1.00[ASN][1000 genomes]
rs3843877	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs4616665	1.00[ASN][1000 genomes]
rs62236134	1.00[ASN][1000 genomes]
rs62236136	1.00[ASN][1000 genomes]
rs6762855	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006471	chr3:21385627-21596955	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1000828	chr3:21399870-21565580	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv536515	chr3:21399870-21565580	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997790	chr3:21516810-21533110	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs161199	CX3CL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21515800-21563000	Weak transcription	Fetal Stomach	stomach
2	chr3:21519800-21549000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:21524000-21537000	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:21526200-21559000	Weak transcription	Aorta	Aorta
5	chr3:21527800-21529400	Enhancers	Pancreatic Islets	Pancreatic Islet

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