Variant report

Variant	rs13421948
Chromosome Location	chr2:187126560-187126561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 195 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:184)

rs_ID	r²[population]
rs10168318	0.81[ASN][1000 genomes]
rs10172511	0.96[ASN][1000 genomes]
rs10186776	0.87[JPT][hapmap]
rs10188807	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10189971	0.94[ASN][1000 genomes]
rs10193268	0.96[ASN][1000 genomes]
rs10193729	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap]
rs10194541	0.96[ASN][1000 genomes]
rs10194719	0.96[ASN][1000 genomes]
rs10196208	0.92[ASN][1000 genomes]
rs10201768	0.88[ASN][1000 genomes]
rs10201874	0.92[ASN][1000 genomes]
rs10203879	0.96[ASN][1000 genomes]
rs10205506	0.94[ASN][1000 genomes]
rs10205705	0.94[ASN][1000 genomes]
rs10210844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1026118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10439308	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10804004	0.85[ASN][1000 genomes]
rs10931239	0.96[ASN][1000 genomes]
rs10931242	0.93[ASN][1000 genomes]
rs10931245	0.80[ASN][1000 genomes]
rs11673938	0.80[ASN][1000 genomes]
rs11676936	0.94[ASN][1000 genomes]
rs11683595	0.93[ASN][1000 genomes]
rs11693737	0.92[ASN][1000 genomes]
rs11884786	0.91[ASN][1000 genomes]
rs11889909	0.94[ASN][1000 genomes]
rs12052331	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12053380	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12463831	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12467212	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467891	0.85[ASN][1000 genomes]
rs12469301	0.89[ASN][1000 genomes]
rs12473542	0.96[ASN][1000 genomes]
rs12475522	0.92[ASN][1000 genomes]
rs12477683	0.95[ASN][1000 genomes]
rs12478370	0.84[ASN][1000 genomes]
rs12611673	0.88[ASN][1000 genomes]
rs12615503	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12619990	0.93[ASN][1000 genomes]
rs12620626	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12623611	0.85[ASN][1000 genomes]
rs12693440	0.91[ASN][1000 genomes]
rs12693444	0.94[ASN][1000 genomes]
rs12693447	0.92[ASN][1000 genomes]
rs12693448	0.94[ASN][1000 genomes]
rs12693449	0.93[ASN][1000 genomes]
rs12993773	0.95[JPT][hapmap]
rs13009502	0.80[ASN][1000 genomes]
rs13015996	0.85[ASN][1000 genomes]
rs13016181	0.84[ASN][1000 genomes]
rs13016273	0.82[ASN][1000 genomes]
rs13017706	0.85[ASN][1000 genomes]
rs13018467	0.85[ASN][1000 genomes]
rs13023992	0.89[ASN][1000 genomes]
rs13024310	0.85[ASN][1000 genomes]
rs13027135	0.96[ASN][1000 genomes]
rs13029473	0.84[ASN][1000 genomes]
rs13029980	0.81[ASN][1000 genomes]
rs13403118	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13409734	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420379	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.80[YRI][hapmap]
rs13421394	0.89[ASN][1000 genomes]
rs13422293	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13426333	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1349154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1375321	0.94[ASN][1000 genomes]
rs1375324	0.96[ASN][1000 genomes]
rs1375325	0.96[ASN][1000 genomes]
rs1375327	0.96[ASN][1000 genomes]
rs1375328	0.96[ASN][1000 genomes]
rs1448851	0.94[ASN][1000 genomes]
rs1448852	0.94[ASN][1000 genomes]
rs1448854	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs1448856	0.85[ASN][1000 genomes]
rs1448858	0.85[ASN][1000 genomes]
rs1448860	0.94[ASN][1000 genomes]
rs1448861	0.96[ASN][1000 genomes]
rs1448863	0.86[ASN][1000 genomes]
rs1562646	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs1562647	0.93[ASN][1000 genomes]
rs16827561	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1839193	0.85[ASN][1000 genomes]
rs1900835	0.90[ASN][1000 genomes]
rs1992930	0.89[ASN][1000 genomes]
rs2197816	0.94[ASN][1000 genomes]
rs2370661	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs2370667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2370675	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2370691	0.94[ASN][1000 genomes]
rs2370692	0.93[ASN][1000 genomes]
rs28498768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3107167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3107177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3107406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3107414	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3112322	0.85[ASN][1000 genomes]
rs33920466	0.83[EUR][1000 genomes]
rs34229945	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35076657	0.83[ASN][1000 genomes]
rs35437667	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4016824	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4130801	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4144822	0.80[ASN][1000 genomes]
rs4144824	0.89[ASN][1000 genomes]
rs4271735	0.82[ASN][1000 genomes]
rs4341896	0.85[ASN][1000 genomes]
rs4430906	0.89[ASN][1000 genomes]
rs4522568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4530331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4535008	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4569437	0.89[ASN][1000 genomes]
rs4608482	0.81[ASN][1000 genomes]
rs4637073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666701	0.96[ASN][1000 genomes]
rs4667079	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4667080	0.99[ASN][1000 genomes]
rs4667081	0.93[ASN][1000 genomes]
rs4667086	0.93[ASN][1000 genomes]
rs4667089	0.89[ASN][1000 genomes]
rs5008098	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56347348	0.86[ASN][1000 genomes]
rs56393956	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56681734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56718299	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56786415	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57289110	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58244659	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58488407	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58579412	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58783284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59087873	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59224241	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59276018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59360834	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60859807	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61083860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61253791	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6434170	0.96[ASN][1000 genomes]
rs6434171	0.94[ASN][1000 genomes]
rs6434179	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs66593320	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6704957	0.86[ASN][1000 genomes]
rs6712627	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6715735	0.89[ASN][1000 genomes]
rs6717965	0.96[ASN][1000 genomes]
rs6726048	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6728734	0.96[ASN][1000 genomes]
rs6740632	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs6741525	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6742943	0.96[ASN][1000 genomes]
rs6743356	0.88[ASN][1000 genomes]
rs6744814	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745187	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6745873	0.96[ASN][1000 genomes]
rs6752407	0.86[ASN][1000 genomes]
rs6754898	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6755955	0.96[ASN][1000 genomes]
rs6759502	0.86[ASN][1000 genomes]
rs6760230	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs67917059	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs716130	0.95[ASN][1000 genomes]
rs72903699	0.81[ASN][1000 genomes]
rs72907565	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73035230	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73035235	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73035261	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7558599	0.93[ASN][1000 genomes]
rs7560019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571191	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7571408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579391	0.88[ASN][1000 genomes]
rs7580038	0.85[ASN][1000 genomes]
rs7586291	0.86[ASN][1000 genomes]
rs7586995	0.83[ASN][1000 genomes]
rs7587077	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7587079	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7599277	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7602918	0.96[ASN][1000 genomes]
rs7606494	0.94[ASN][1000 genomes]
rs980540	0.94[ASN][1000 genomes]
rs9807987	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1002243	chr2:186692815-187150225	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv536077	chr2:186692815-187150225	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv875548	chr2:186798249-187164657	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1003369	chr2:186980675-187133740	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1014726	chr2:187036909-187213113	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv536078	chr2:187036909-187213113	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3434695	chr2:187126495-187148916	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13421948	ITGAV	cis	cerebellum	SCAN
rs13421948	ITGAV	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187120200-187139000	Weak transcription	Gastric	stomach
2	chr2:187122200-187128000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:187122800-187128200	Weak transcription	Ovary	ovary
4	chr2:187126400-187126600	ZNF genes & repeats	Spleen	Spleen
5	chr2:187126400-187127000	ZNF genes & repeats	Fetal Intestine Small	intestine

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