Variant report

Variant	rs2299123
Chromosome Location	chr7:39488735-39488736
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10239767	0.86[CEU][hapmap]
rs10239968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10242113	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10249501	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10254703	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10258812	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10261831	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10267900	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10268273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10269203	0.88[CEU][hapmap]
rs10269280	0.82[CEU][hapmap]
rs10271873	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272392	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1155269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11769625	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11970896	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11972350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11979059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12112809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12531581	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12536665	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17769607	0.86[CEU][hapmap]
rs1860115	0.82[CEU][hapmap]
rs2073540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2073541	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2073542	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2073543	0.95[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2073544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2073546	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs2108719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2190888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2190889	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2190890	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs2190891	0.82[CEU][hapmap]
rs2215138	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs2237368	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237369	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237372	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237373	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2237374	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2237376	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237377	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237379	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237381	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237385	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237389	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2237390	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237391	0.81[CEU][hapmap]
rs2237395	0.87[CEU][hapmap]
rs2282916	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299121	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299122	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2299126	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299127	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2299128	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2299129	0.82[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2299132	0.82[CEU][hapmap]
rs2299133	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs2302122	0.95[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2302123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302125	0.95[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28473216	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28625432	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28627325	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28651247	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2876836	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2876837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876838	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2876839	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34731084	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35650049	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778933	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3819413	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3819414	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819415	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819417	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819418	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819419	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819420	0.82[CEU][hapmap]
rs3819421	0.82[CEU][hapmap]
rs3819422	0.82[CEU][hapmap]
rs3819426	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs3823618	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419726	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4535636	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4554374	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4629765	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56132347	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58810887	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59085311	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60003380	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60259745	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61101006	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6462917	0.82[CEU][hapmap]
rs67717647	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6947429	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6947866	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948191	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948501	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6966246	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6977512	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs740510	0.95[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs7459210	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs7797301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801100	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs887015	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv966782	chr7:39454992-39581886	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299123	HECW1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39473000-39498000	Weak transcription	Pancreas	Pancrea
2	chr7:39485800-39502000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:39486800-39491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:39488400-39499400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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