Variant report

Variant	rs4699496
Chromosome Location	chr4:97185259-97185260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10002816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10006557	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10007900	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10015613	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10016180	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10021889	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10213429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10856919	0.80[ASN][1000 genomes]
rs11097501	0.90[ASN][1000 genomes]
rs11097502	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097505	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11932384	0.90[ASN][1000 genomes]
rs11935830	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12499067	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12501360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12508802	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12509883	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12642471	0.92[ASN][1000 genomes]
rs12644982	0.90[ASN][1000 genomes]
rs12650441	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13104802	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13121458	0.90[ASN][1000 genomes]
rs13122821	0.90[ASN][1000 genomes]
rs13122856	0.91[ASN][1000 genomes]
rs13150508	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1354704	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1354706	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1373331	0.84[ASN][1000 genomes]
rs1395199	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1425361	0.82[ASN][1000 genomes]
rs1444021	0.90[ASN][1000 genomes]
rs1506304	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1506305	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1506306	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1506317	0.88[ASN][1000 genomes]
rs1506318	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1506319	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1506320	0.85[ASN][1000 genomes]
rs1506321	0.88[ASN][1000 genomes]
rs1567036	0.86[ASN][1000 genomes]
rs1605227	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17025493	0.84[ASN][1000 genomes]
rs1834360	0.82[ASN][1000 genomes]
rs1847963	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1847964	0.82[ASN][1000 genomes]
rs1847966	0.90[ASN][1000 genomes]
rs1847967	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1847968	0.86[ASN][1000 genomes]
rs1847969	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1857889	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1857890	0.86[ASN][1000 genomes]
rs1867400	0.90[ASN][1000 genomes]
rs1911074	0.85[ASN][1000 genomes]
rs1911076	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1911077	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1948912	0.85[ASN][1000 genomes]
rs2048022	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2083922	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2113973	0.90[ASN][1000 genomes]
rs2174584	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2197322	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs28407945	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28523416	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28565871	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28633781	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2865736	0.85[ASN][1000 genomes]
rs28788633	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35257138	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36039803	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4146410	0.85[ASN][1000 genomes]
rs4146411	0.85[ASN][1000 genomes]
rs4293790	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4343731	0.92[ASN][1000 genomes]
rs4414959	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4611939	0.85[ASN][1000 genomes]
rs4613576	0.85[ASN][1000 genomes]
rs4619895	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699283	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4699285	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699287	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4699288	0.84[ASN][1000 genomes]
rs4699485	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699501	0.85[ASN][1000 genomes]
rs4699503	0.84[ASN][1000 genomes]
rs4699512	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699513	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5017329	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55680326	0.89[ASN][1000 genomes]
rs60275360	0.92[ASN][1000 genomes]
rs6532596	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532597	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532600	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6815558	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6815743	0.88[ASN][1000 genomes]
rs6816447	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6820075	0.92[ASN][1000 genomes]
rs6826156	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6826817	0.82[ASN][1000 genomes]
rs6830120	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6832934	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6835808	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837318	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841294	0.85[ASN][1000 genomes]
rs6855768	0.84[ASN][1000 genomes]
rs6857113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72880179	0.82[ASN][1000 genomes]
rs72880182	0.82[ASN][1000 genomes]
rs72883800	0.85[ASN][1000 genomes]
rs72885446	0.84[ASN][1000 genomes]
rs7653937	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs766061	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7671604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673756	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7676317	0.84[ASN][1000 genomes]
rs7676764	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7686174	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7690397	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9307167	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307168	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs931841	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs931842	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9686051	0.82[AMR][1000 genomes]
rs9884259	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9884940	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9998383	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9999006	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830013	chr4:97033125-97204291	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1003868	chr4:97068155-97222544	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv470057	chr4:97104880-97311657	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv461589	chr4:97104881-97311657	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv594916	chr4:97104881-97311657	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv879631	chr4:97114706-97263153	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv879632	chr4:97118539-97308914	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879633	chr4:97125086-97263153	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2763381	chr4:97140746-97193871	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4699496	RAP1GDS1	cis	parietal	SCAN
rs4699496	DAPP1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:97182600-97186600	Weak transcription	Fetal Brain Male	brain
2	chr4:97183600-97187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:97185000-97185400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:97185000-97185600	Enhancers	Fetal Intestine Large	intestine

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