Variant report

Variant	rs6508841
Chromosome Location	chr19:39514844-39514845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10406222	0.84[ASN][1000 genomes]
rs10416823	0.92[ASN][1000 genomes]
rs10417436	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs10424827	0.90[ASN][1000 genomes]
rs10426645	0.92[ASN][1000 genomes]
rs10426661	0.81[ASN][1000 genomes]
rs1062261	0.86[ASN][1000 genomes]
rs10853723	0.92[ASN][1000 genomes]
rs10853724	0.92[ASN][1000 genomes]
rs11083499	0.89[ASN][1000 genomes]
rs11083500	0.91[ASN][1000 genomes]
rs11083501	0.92[ASN][1000 genomes]
rs11083502	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1139251	0.86[ASN][1000 genomes]
rs11667641	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs11670486	0.92[ASN][1000 genomes]
rs11670520	0.89[ASN][1000 genomes]
rs11673044	0.83[ASN][1000 genomes]
rs11673637	0.86[ASN][1000 genomes]
rs11880441	0.92[ASN][1000 genomes]
rs11883422	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs12609806	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs12610200	0.86[ASN][1000 genomes]
rs12610248	0.86[ASN][1000 genomes]
rs12971842	0.96[ASN][1000 genomes]
rs12972850	0.90[ASN][1000 genomes]
rs12972978	0.94[ASN][1000 genomes]
rs12978163	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978749	0.93[ASN][1000 genomes]
rs12982199	0.89[ASN][1000 genomes]
rs12982349	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982529	0.97[ASN][1000 genomes]
rs12985447	0.97[ASN][1000 genomes]
rs1840745	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1840746	0.90[ASN][1000 genomes]
rs1840747	0.90[ASN][1000 genomes]
rs1840748	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs1864191	0.87[ASN][1000 genomes]
rs1869983	0.90[ASN][1000 genomes]
rs2318896	0.83[YRI][hapmap]
rs36154890	0.92[ASN][1000 genomes]
rs3848623	0.91[ASN][1000 genomes]
rs4280369	0.92[ASN][1000 genomes]
rs4802007	0.91[ASN][1000 genomes]
rs4802009	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803181	0.86[ASN][1000 genomes]
rs4803185	0.92[ASN][1000 genomes]
rs4803186	0.92[ASN][1000 genomes]
rs4803187	0.92[ASN][1000 genomes]
rs4803188	0.90[ASN][1000 genomes]
rs4803193	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs58897626	0.83[ASN][1000 genomes]
rs60775146	0.83[ASN][1000 genomes]
rs62119538	0.84[ASN][1000 genomes]
rs628335	0.80[ASN][1000 genomes]
rs649150	0.82[CEU][hapmap]
rs6508835	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508836	0.92[ASN][1000 genomes]
rs6508837	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508838	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508839	0.97[ASN][1000 genomes]
rs6508840	0.97[ASN][1000 genomes]
rs6508842	0.92[ASN][1000 genomes]
rs6508843	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs681496	0.83[ASN][1000 genomes]
rs7247801	0.92[ASN][1000 genomes]
rs7248513	0.92[ASN][1000 genomes]
rs7248652	0.92[ASN][1000 genomes]
rs7250110	0.83[ASN][1000 genomes]
rs7250431	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs7251264	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7255211	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256126	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258182	0.87[YRI][hapmap]
rs7258862	0.90[ASN][1000 genomes]
rs7259064	0.81[ASN][1000 genomes]
rs7259197	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs7259473	0.82[ASN][1000 genomes]
rs7259801	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs8100503	0.83[ASN][1000 genomes]
rs8103187	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104751	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs8104899	0.92[ASN][1000 genomes]
rs8104990	0.92[ASN][1000 genomes]
rs8105865	0.92[ASN][1000 genomes]
rs8109176	0.86[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6508841	DYRK1B	cis	cerebellum	SCAN
rs6508841	OPA3	cis	cerebellum	SCAN
rs6508841	B3GNT8	cis	cerebellum	SCAN
rs6508841	ZNF576	cis	cerebellum	SCAN
rs6508841	ZNF526	cis	parietal	SCAN
rs6508841	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39481000-39516000	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39487200-39518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39496600-39515800	Weak transcription	Ovary	ovary
4	chr19:39498400-39516600	Weak transcription	A549	lung
5	chr19:39499400-39516600	Weak transcription	Brain Anterior Caudate	brain
6	chr19:39499800-39516800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:39500000-39515600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:39501800-39515800	Weak transcription	Adipose Nuclei	Adipose
9	chr19:39502000-39515400	Weak transcription	Fetal Intestine Small	intestine
10	chr19:39502200-39515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:39502400-39518000	Weak transcription	Aorta	Aorta
12	chr19:39503000-39515400	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:39503600-39520200	Weak transcription	Liver	Liver
14	chr19:39504800-39515800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr19:39505200-39515600	Weak transcription	Esophagus	oesophagus
16	chr19:39506800-39515600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:39506800-39517200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:39507200-39517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:39507400-39515600	Weak transcription	Fetal Stomach	stomach
20	chr19:39510600-39516800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:39511000-39515000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:39511200-39517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:39512400-39518000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:39512800-39515000	Weak transcription	GM12878-XiMat	blood
25	chr19:39513000-39521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:39513000-39521600	Weak transcription	Right Atrium	heart
27	chr19:39513200-39517400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:39513600-39517400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:39514000-39515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:39514000-39516200	Enhancers	K562	blood
31	chr19:39514000-39517600	Weak transcription	NHEK	skin
32	chr19:39514000-39521400	Weak transcription	Pancreas	Pancrea
33	chr19:39514000-39522200	Weak transcription	Gastric	stomach
34	chr19:39514200-39517800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:39514200-39517800	Weak transcription	Placenta	Placenta
36	chr19:39514400-39517400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:39514400-39517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:39514400-39517800	Weak transcription	Brain Germinal Matrix	brain
39	chr19:39514400-39517800	Weak transcription	Left Ventricle	heart
40	chr19:39514400-39520400	Weak transcription	Fetal Intestine Large	intestine
41	chr19:39514400-39521600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:39514400-39521800	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:39514600-39517600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:39514600-39517600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr19:39514600-39521400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:39514800-39517600	Weak transcription	Lung	lung
47	chr19:39514800-39518600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:39514800-39519600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:39514800-39520000	Strong transcription	Brain Cingulate Gyrus	brain

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