Variant report

Variant	rs2909109
Chromosome Location	chr19:38169355-38169356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10402671	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10403173	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10404031	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs10406379	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs10408619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10409605	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10412510	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10417576	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10420268	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10420552	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10420746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083432	0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap]
rs11673023	0.82[ASN][1000 genomes]
rs12459015	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1291	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs12974225	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs12979640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13744	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1531549	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1564208	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap]
rs16958861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16958863	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1974714	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1975937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1975939	0.82[AMR][1000 genomes]
rs2075281	0.81[CHB][hapmap]
rs2075284	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2279148	0.95[CHB][hapmap]
rs2279149	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2287229	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2291002	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs2291004	0.82[ASW][hapmap]
rs2385119	0.80[ASN][1000 genomes]
rs241932	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs241950	0.81[ASN][1000 genomes]
rs28512414	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2909085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909088	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909093	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2909098	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2909100	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2909102	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2909105	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2927739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2927740	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2927742	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2927746	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2927747	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2972430	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2972434	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2972437	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2972438	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2972439	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2972445	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2972446	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2972447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2972448	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972452	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2972458	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3095724	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3095726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3101746	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3101747	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3112433	0.95[ASN][1000 genomes]
rs3112434	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35863684	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3829688	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4802024	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4802029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4802135	0.86[CHB][hapmap]
rs4803231	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4803233	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4803262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4803263	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4803276	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4803287	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4803524	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs56151076	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508736	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8100646	0.87[ASN][1000 genomes]
rs8102579	0.81[CHB][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs8103633	0.87[ASN][1000 genomes]
rs8103647	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8109038	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs8110865	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8112706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs856300	1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs856304	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs9304568	0.84[ASN][1000 genomes]
rs954504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs958305	0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs968073	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9749368	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9941475	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2909109	HIF3A	cis	parietal	SCAN
rs2909109	APOE	cis	cerebellum	SCAN
rs2909109	ZNF45	cis	cerebellum	SCAN
rs2909109	ZNF404	cis	parietal	SCAN
rs2909109	NOVA2	cis	parietal	SCAN
rs2909109	SIX5	cis	cerebellum	SCAN
rs2909109	DMPK	cis	parietal	SCAN
rs2909109	PHLDB3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38166600-38182600	Weak transcription	Right Ventricle	heart
2	chr19:38166800-38171400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38166800-38180000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:38167000-38170400	ZNF genes & repeats	Liver	Liver
5	chr19:38167000-38171400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:38167400-38170600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr19:38167400-38171600	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:38167600-38170400	ZNF genes & repeats	Brain Angular Gyrus	brain
9	chr19:38167600-38170400	ZNF genes & repeats	Brain Hippocampus Middle	brain
10	chr19:38167800-38169400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:38168600-38170400	ZNF genes & repeats	Fetal Lung	lung
12	chr19:38168600-38170400	ZNF genes & repeats	Dnd41	blood
13	chr19:38168600-38171400	ZNF genes & repeats	Aorta	Aorta
14	chr19:38168600-38171600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:38168600-38171600	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr19:38168800-38170000	ZNF genes & repeats	Spleen	Spleen
17	chr19:38168800-38170200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
18	chr19:38168800-38171400	ZNF genes & repeats	Left Ventricle	heart
19	chr19:38168800-38172200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:38168800-38172600	ZNF genes & repeats	Fetal Stomach	stomach
21	chr19:38169000-38169800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:38169000-38170600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:38169200-38170000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:38169200-38170400	ZNF genes & repeats	Brain Substantia Nigra	brain
25	chr19:38169200-38170400	ZNF genes & repeats	Ovary	ovary

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