Variant report

Variant	rs13397537
Chromosome Location	chr2:189737535-189737536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189733529..189735881-chr2:189735905..189738655,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10048793	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10170845	1.00[EUR][1000 genomes]
rs10177387	0.98[AFR][1000 genomes]
rs10185102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10194182	0.98[AFR][1000 genomes]
rs10196959	0.83[AFR][1000 genomes]
rs10207990	0.98[AFR][1000 genomes]
rs10445725	1.00[EUR][1000 genomes]
rs10445726	1.00[EUR][1000 genomes]
rs11674580	0.96[EUR][1000 genomes]
rs11676244	0.96[EUR][1000 genomes]
rs11678718	0.96[EUR][1000 genomes]
rs11681365	0.96[EUR][1000 genomes]
rs11682895	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11684224	0.96[EUR][1000 genomes]
rs11687872	0.96[EUR][1000 genomes]
rs11695250	0.92[EUR][1000 genomes]
rs11695327	0.96[EUR][1000 genomes]
rs13410823	0.95[AFR][1000 genomes]
rs34587834	0.96[EUR][1000 genomes]
rs56934493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57351486	0.96[EUR][1000 genomes]
rs57832802	0.96[EUR][1000 genomes]
rs58108785	0.96[EUR][1000 genomes]
rs58210062	0.96[EUR][1000 genomes]
rs60162413	0.96[EUR][1000 genomes]
rs60307701	0.96[EUR][1000 genomes]
rs60514585	0.96[EUR][1000 genomes]
rs60602630	0.96[EUR][1000 genomes]
rs60608780	0.96[EUR][1000 genomes]
rs60916684	0.96[EUR][1000 genomes]
rs61011178	0.96[EUR][1000 genomes]
rs6434300	0.95[AFR][1000 genomes]
rs6709783	0.95[AFR][1000 genomes]
rs6710225	0.95[AFR][1000 genomes]
rs6746832	0.95[AFR][1000 genomes]
rs6752196	0.95[AFR][1000 genomes]
rs6760322	0.95[AFR][1000 genomes]
rs72902633	0.96[EUR][1000 genomes]
rs72902639	0.96[EUR][1000 genomes]
rs72902642	0.96[EUR][1000 genomes]
rs72902649	0.96[EUR][1000 genomes]
rs72902655	0.96[EUR][1000 genomes]
rs72902678	0.96[EUR][1000 genomes]
rs72902691	0.96[EUR][1000 genomes]
rs72904650	0.96[EUR][1000 genomes]
rs72904664	0.96[EUR][1000 genomes]
rs72904665	0.96[EUR][1000 genomes]
rs72904686	0.96[EUR][1000 genomes]
rs72904689	0.96[EUR][1000 genomes]
rs72904690	0.96[EUR][1000 genomes]
rs72904691	0.96[EUR][1000 genomes]
rs72904695	0.96[EUR][1000 genomes]
rs72904696	0.96[EUR][1000 genomes]
rs72904698	0.96[EUR][1000 genomes]
rs72904701	0.96[EUR][1000 genomes]
rs72904702	0.96[EUR][1000 genomes]
rs72906605	0.96[EUR][1000 genomes]
rs72906607	0.96[EUR][1000 genomes]
rs72906611	0.96[EUR][1000 genomes]
rs72906616	0.96[EUR][1000 genomes]
rs72906620	0.96[EUR][1000 genomes]
rs72906621	0.96[EUR][1000 genomes]
rs72906631	0.96[EUR][1000 genomes]
rs72906633	0.96[EUR][1000 genomes]
rs72906638	0.96[EUR][1000 genomes]
rs72906640	0.96[EUR][1000 genomes]
rs72906643	0.96[EUR][1000 genomes]
rs72906646	0.96[EUR][1000 genomes]
rs72906655	0.96[EUR][1000 genomes]
rs72906657	0.96[EUR][1000 genomes]
rs72906662	0.96[EUR][1000 genomes]
rs72906664	0.96[EUR][1000 genomes]
rs72906691	0.96[EUR][1000 genomes]
rs72906692	0.96[EUR][1000 genomes]
rs72906695	0.96[EUR][1000 genomes]
rs72906698	0.96[EUR][1000 genomes]
rs72908623	1.00[EUR][1000 genomes]
rs72908644	1.00[EUR][1000 genomes]
rs72908645	1.00[EUR][1000 genomes]
rs72908648	1.00[EUR][1000 genomes]
rs72908650	1.00[EUR][1000 genomes]
rs72908658	1.00[EUR][1000 genomes]
rs72908661	1.00[EUR][1000 genomes]
rs72908663	0.96[EUR][1000 genomes]
rs7355414	1.00[MEX][hapmap]
rs7565039	0.96[EUR][1000 genomes]
rs7566920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7593672	0.98[AFR][1000 genomes]
rs7593834	0.98[AFR][1000 genomes]
rs7603795	0.95[AFR][1000 genomes]
rs7607507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9288161	0.98[AFR][1000 genomes]
rs972470	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1008847	chr2:189603961-189769705	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv4236	chr2:189730546-189740139	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv821858	chr2:189733808-189740029	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13397537	SH2D2A	trans	brain	seeQTL
rs13397537	MTNR1A	trans	brain	seeQTL
rs13397537	CRX	trans	brain	seeQTL
rs13397537	GDF10	trans	brain	seeQTL
rs13397537	GUCA1C	trans	brain	seeQTL
rs13397537	SLC5A7	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189735200-189740000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:189737200-189743200	Weak transcription	Fetal Lung	lung

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