Variant report

Variant	rs1019290
Chromosome Location	chr7:38506889-38506890
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1014570	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs1014572	0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs1019288	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1030018	0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs10951557	0.85[YRI][hapmap];0.98[AFR][1000 genomes]
rs12531584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535314	0.93[YRI][hapmap];1.00[AFR][1000 genomes]
rs12670885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17171372	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17171383	0.85[YRI][hapmap];0.96[AFR][1000 genomes]
rs2043785	0.89[MKK][hapmap];0.80[YRI][hapmap]
rs2196679	0.93[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs2284255	0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs2392577	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3807417	0.93[YRI][hapmap];0.96[AFR][1000 genomes]
rs3807420	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs3807421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723760	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs6462846	0.91[LWK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs6462847	0.93[LWK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs67521118	0.80[ASN][1000 genomes]
rs6950276	0.85[YRI][hapmap];0.98[AFR][1000 genomes]
rs6969360	0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs6970073	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs6972241	0.93[YRI][hapmap];0.96[AFR][1000 genomes]
rs722335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722336	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7777361	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs7791266	0.89[AFR][1000 genomes]
rs7808755	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs7809200	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs7811329	1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.96[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	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv1825425	chr7:38457144-38507180	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019290	AMPH	cis	parietal	SCAN
rs1019290	EEPD1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38499800-38523600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:38501000-38522400	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:38501800-38522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:38502000-38512200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
6	chr7:38502800-38533800	Weak transcription	Aorta	Aorta
7	chr7:38503800-38522400	Weak transcription	Fetal Lung	lung
8	chr7:38504000-38508000	Weak transcription	Brain Angular Gyrus	brain
9	chr7:38504000-38513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:38504200-38514600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:38506600-38507000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:38506600-38507200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:38506800-38507000	Enhancers	Left Ventricle	heart

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