Variant report

Variant	rs4799639
Chromosome Location	chr18:29787900-29787901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12457952	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12458880	0.88[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs16962825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs173032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17663127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17743259	0.82[JPT][hapmap]
rs193095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2241891	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335514	0.91[ASN][1000 genomes]
rs335515	0.98[ASN][1000 genomes]
rs335516	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs335517	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs335518	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs335519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4799640	0.88[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs57787388	0.81[ASN][1000 genomes]
rs59324074	0.94[ASN][1000 genomes]
rs62095611	0.91[ASN][1000 genomes]
rs6506962	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244677	0.98[ASN][1000 genomes]
rs7245136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9948943	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4799639	TTR	cis	parietal	SCAN
rs4799639	RNF138	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29784600-29795200	Enhancers	Fetal Intestine Large	intestine
2	chr18:29786800-29791200	Enhancers	Liver	Liver
3	chr18:29786800-29795200	Enhancers	Fetal Intestine Small	intestine
4	chr18:29787200-29790400	Enhancers	Duodenum Mucosa	Duodenum
5	chr18:29787400-29788800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr18:29787400-29789000	Enhancers	Rectal Mucosa Donor 29	rectum

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