Variant report

Variant	rs2199308
Chromosome Location	chr4:87099337-87099338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10003556	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10003756	0.88[ASN][1000 genomes]
rs10004539	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10009161	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10010011	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs10016847	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019871	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022904	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10026060	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10026338	0.88[ASN][1000 genomes]
rs10029339	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10034428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10213302	0.92[ASN][1000 genomes]
rs10213451	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10213453	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10516769	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1108429	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11097101	0.92[ASN][1000 genomes]
rs11097102	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097103	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11935211	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12500319	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12640392	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12646076	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12650052	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1460750	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460758	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460759	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460760	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460761	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1460763	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599313	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599314	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17011421	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011460	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17011540	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17011547	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17011564	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17011584	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17011588	0.88[ASN][1000 genomes]
rs17011592	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17011654	0.82[JPT][hapmap]
rs17011655	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1903360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903361	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2035056	0.90[ASN][1000 genomes]
rs2035057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2199309	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28425193	0.88[ASN][1000 genomes]
rs28583812	0.88[ASN][1000 genomes]
rs28642002	0.92[ASN][1000 genomes]
rs2869421	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869422	0.88[ASN][1000 genomes]
rs28722990	0.88[ASN][1000 genomes]
rs28791572	0.88[ASN][1000 genomes]
rs28803851	0.90[ASN][1000 genomes]
rs28812808	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28830922	0.90[ASN][1000 genomes]
rs28839895	0.92[ASN][1000 genomes]
rs28870188	0.88[ASN][1000 genomes]
rs28896887	0.92[ASN][1000 genomes]
rs2904090	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4114893	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4132490	0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs4561895	0.92[ASN][1000 genomes]
rs59124829	0.92[ASN][1000 genomes]
rs6531905	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531906	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531907	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531909	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531910	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531911	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67768527	0.88[ASN][1000 genomes]
rs6814005	0.84[ASN][1000 genomes]
rs6817452	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825521	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826951	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827405	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827698	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6828947	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829870	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832259	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6844363	0.85[JPT][hapmap]
rs6844365	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845605	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845742	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7440491	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655797	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7657056	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7663388	0.92[ASN][1000 genomes]
rs7663763	0.92[ASN][1000 genomes]
rs7668374	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7669487	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678480	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7680934	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7685419	0.88[ASN][1000 genomes]
rs7685683	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7687771	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7695707	0.92[ASN][1000 genomes]
rs7699047	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307016	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs9654155	0.92[ASN][1000 genomes]
rs9884127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9994303	0.88[ASN][1000 genomes]
rs9996693	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997633	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9999403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005338	chr4:87023398-87108555	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2757070	chr4:87075759-87138765	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2759263	chr4:87075759-87138765	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2199308	HELQ	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87052000-87114200	Weak transcription	Ovary	ovary
2	chr4:87078000-87113400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:87095800-87105600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87097400-87101800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:87098600-87100000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:87099200-87099600	Enhancers	Hela-S3	cervix

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