Variant report

Variant	rs2909088
Chromosome Location	chr19:38176548-38176549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10402671	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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];0.87[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];0.84[ASN][1000 genomes]
rs10409605	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10412510	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10417576	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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];0.81[ASN][1000 genomes]
rs11673023	0.83[ASN][1000 genomes]
rs12459015	0.84[ASN][1000 genomes]
rs1291	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[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];0.85[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];1.00[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];0.87[ASN][1000 genomes]
rs1531549	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[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];0.87[AFR][1000 genomes];0.96[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];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1974714	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1975937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1975939	0.82[AMR][1000 genomes]
rs2075281	0.81[CHB][hapmap]
rs2075284	0.95[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];0.96[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]
rs241932	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs241950	0.81[ASN][1000 genomes]
rs28512414	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2909085	0.96[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];0.95[AFR][1000 genomes];0.94[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];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2909100	0.87[AFR][1000 genomes];0.88[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];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[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];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2909109	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]
rs2927739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2927742	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2927746	0.96[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];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2972430	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2972434	0.95[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];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2972438	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[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];0.88[AFR][1000 genomes];0.90[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];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2972445	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2972446	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2972447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972452	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2972458	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3095724	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3095726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3101746	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3101747	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3112433	0.94[ASN][1000 genomes]
rs3112434	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35863684	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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];0.87[ASN][1000 genomes]
rs4802024	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[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];0.83[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];0.81[ASN][1000 genomes]
rs4803233	0.82[AMR][1000 genomes];0.83[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];0.87[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];0.98[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	0.88[ASN][1000 genomes]
rs8103647	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8109038	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs8110865	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8112706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[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];0.85[ASN][1000 genomes]
rs856304	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs9304568	0.83[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];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9749368	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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
rs2909088	SIX5	cis	cerebellum	SCAN
rs2909088	HIF3A	cis	parietal	SCAN
rs2909088	ZNF45	cis	cerebellum	SCAN
rs2909088	APOE	cis	cerebellum	SCAN
rs2909088	NOVA2	cis	parietal	SCAN
rs2909088	DMPK	cis	parietal	SCAN
rs2909088	PHLDB3	cis	parietal	SCAN
rs2909088	ZNF404	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38166600-38182600	Weak transcription	Right Ventricle	heart
2	chr19:38166800-38180000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:38169800-38182200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:38170400-38176600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr19:38170400-38177000	Weak transcription	Brain Anterior Caudate	brain
6	chr19:38170400-38177200	Weak transcription	Psoas Muscle	Psoas
7	chr19:38170400-38182200	Weak transcription	Brain Substantia Nigra	brain
8	chr19:38170600-38182200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:38170800-38182200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:38171400-38182200	Weak transcription	Brain Angular Gyrus	brain
11	chr19:38172800-38177000	Weak transcription	Brain Germinal Matrix	brain
12	chr19:38172800-38182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:38173000-38176600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:38173600-38182800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:38173800-38177000	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:38173800-38180400	Weak transcription	Dnd41	blood
17	chr19:38173800-38182200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:38173800-38182200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:38174600-38182200	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:38175000-38182400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:38175200-38176600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38175200-38177200	Weak transcription	Ovary	ovary
23	chr19:38175200-38177400	Weak transcription	Left Ventricle	heart
24	chr19:38175200-38179400	Weak transcription	Fetal Stomach	stomach
25	chr19:38175200-38182400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:38175800-38182200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:38176200-38177800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:38176400-38176800	ZNF genes & repeats	Fetal Lung	lung
29	chr19:38176400-38177600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr19:38176400-38179800	ZNF genes & repeats	Fetal Brain Female	brain
31	chr19:38176400-38180400	Weak transcription	Fetal Brain Male	brain
32	chr19:38176400-38182200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:38176400-38182400	Weak transcription	Aorta	Aorta

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