Variant report

Variant	rs17109073
Chromosome Location	chr14:39723162-39723163
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39720805..39723353-chr14:39735805..39738506,2	K562	blood:
2	chr14:39717370..39718891-chr14:39721042..39723991,2	K562	blood:

Variant related genes	Relation type
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10131617	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10133417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10134143	0.87[ASN][1000 genomes]
rs10134365	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10137352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10137905	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs10138024	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10138869	0.91[JPT][hapmap]
rs10151659	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10162550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872920	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs11157053	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs11157058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11620695	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11621264	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11621330	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11621822	0.88[ASN][1000 genomes]
rs11624839	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11626150	0.87[ASN][1000 genomes]
rs11626679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11627580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628075	0.86[ASN][1000 genomes]
rs11845046	0.90[ASN][1000 genomes]
rs12434140	0.95[JPT][hapmap]
rs12587713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588386	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12588728	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12589831	0.88[ASN][1000 genomes]
rs12590172	0.80[JPT][hapmap]
rs12882709	0.88[ASN][1000 genomes]
rs12883781	0.80[ASN][1000 genomes]
rs12892482	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12894855	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs12894960	0.82[ASN][1000 genomes]
rs12896838	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1594842	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17109021	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109028	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109056	0.90[ASN][1000 genomes]
rs1897792	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs1950952	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1998194	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2082635	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2274395	0.86[JPT][hapmap]
rs2274396	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs2274399	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28626340	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28680827	0.86[ASN][1000 genomes]
rs35065854	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35184650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35201135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35613410	0.88[ASN][1000 genomes]
rs3814860	0.86[JPT][hapmap]
rs4902528	0.91[JPT][hapmap]
rs4902569	0.90[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902570	0.90[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902622	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4902648	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6571919	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7140164	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7143646	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7148150	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7150735	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7152341	0.86[JPT][hapmap]
rs7153482	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7161403	0.82[JPT][hapmap]
rs719455	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs8004348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8006321	0.86[JPT][hapmap]
rs8018717	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs910370	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs956108	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs956109	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9671943	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9671953	0.82[EUR][1000 genomes];0.81[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	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17109073	PPP2R3C	cis	parietal	SCAN
rs17109073	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39703600-39735400	Weak transcription	Pancreas	Pancrea
2	chr14:39704400-39734400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr14:39718600-39728000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:39721600-39724200	Strong transcription	Fetal Intestine Large	intestine
5	chr14:39721600-39725200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:39721600-39728000	Weak transcription	Fetal Intestine Small	intestine
7	chr14:39721800-39723400	Weak transcription	HepG2	liver
8	chr14:39722800-39726000	Weak transcription	Liver	Liver

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