Variant report

Variant	rs10416089
Chromosome Location	chr19:43002369-43002370
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10084159	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10401271	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10402361	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10402401	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10402677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10403517	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10403979	0.89[ASN][1000 genomes]
rs10404402	0.88[ASN][1000 genomes]
rs10404509	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10405445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10405646	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10405906	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10407178	0.89[ASN][1000 genomes]
rs10407576	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10410147	0.89[ASN][1000 genomes]
rs10411165	0.89[ASN][1000 genomes]
rs10411458	0.94[ASN][1000 genomes]
rs10412463	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10413014	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10413413	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10414602	0.89[ASN][1000 genomes]
rs10415564	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10417418	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10417693	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10419378	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420164	0.89[ASN][1000 genomes]
rs10420796	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10421108	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10421620	0.89[ASN][1000 genomes]
rs10421881	0.89[ASN][1000 genomes]
rs10422283	0.85[CHB][hapmap]
rs10422573	0.86[ASN][1000 genomes]
rs10422987	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10423291	0.94[ASN][1000 genomes]
rs10469271	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10469284	0.92[EUR][1000 genomes]
rs10469285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1076243	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083659	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11665767	0.89[ASN][1000 genomes]
rs11665870	0.88[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11665935	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11666350	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11666425	0.89[ASN][1000 genomes]
rs11666835	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666862	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668009	0.89[ASN][1000 genomes]
rs11668460	0.89[ASN][1000 genomes]
rs11668599	0.84[EUR][1000 genomes]
rs11669892	0.85[ASN][1000 genomes]
rs11670316	0.89[ASN][1000 genomes]
rs11671272	0.92[EUR][1000 genomes]
rs11671846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11673645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673684	0.89[ASN][1000 genomes]
rs11879306	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11881517	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11882150	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11882882	0.85[ASN][1000 genomes]
rs12327586	0.89[ASN][1000 genomes]
rs12611218	0.81[EUR][1000 genomes]
rs13343936	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13346414	0.89[ASN][1000 genomes]
rs16975789	0.84[EUR][1000 genomes]
rs16975865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16975890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859341	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2267631	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28411988	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28447294	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2883270	0.85[ASN][1000 genomes]
rs4080606	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4499340	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55641435	0.94[ASN][1000 genomes]
rs55850134	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56237547	0.89[ASN][1000 genomes]
rs56978333	0.81[ASN][1000 genomes]
rs57902582	0.86[ASN][1000 genomes]
rs59525393	0.85[ASN][1000 genomes]
rs60313903	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60662795	0.92[ASN][1000 genomes]
rs6509016	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6509017	0.94[ASN][1000 genomes]
rs6509020	0.89[ASN][1000 genomes]
rs7247618	0.89[ASN][1000 genomes]
rs7248042	0.85[ASN][1000 genomes]
rs7248297	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249411	0.85[ASN][1000 genomes]
rs7253056	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7253209	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8102439	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8102519	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103285	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103891	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106083	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8106570	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8107790	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8108816	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8108844	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs8110766	0.89[ASN][1000 genomes]
rs8110917	0.89[ASN][1000 genomes]
rs8112156	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs851298	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851301	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851302	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304604	0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42997000-43003800	Enhancers	Fetal Intestine Small	intestine
2	chr19:42998000-43004800	Enhancers	Fetal Intestine Large	intestine
3	chr19:42999600-43003400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:43000000-43003000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr19:43000400-43003000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:43000400-43003000	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:43000600-43002600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr19:43000600-43003600	Enhancers	Fetal Kidney	kidney
9	chr19:43000600-43003800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:43000800-43003000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:43000800-43003200	Enhancers	Primary B cells from cord blood	blood
12	chr19:43000800-43003400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr19:43000800-43003400	Enhancers	Small Intestine	intestine
14	chr19:43001000-43002800	Enhancers	Adipose Nuclei	Adipose
15	chr19:43001000-43003200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:43001000-43003600	Enhancers	Brain Hippocampus Middle	brain
17	chr19:43001200-43002600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:43001200-43003800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:43001400-43002600	Flanking Active TSS	GM12878-XiMat	blood
20	chr19:43001400-43002800	Enhancers	Fetal Lung	lung
21	chr19:43001400-43003000	Flanking Active TSS	HepG2	liver
22	chr19:43001400-43003200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr19:43001400-43003600	Enhancers	Brain Anterior Caudate	brain
24	chr19:43001400-43003600	Enhancers	Brain Cingulate Gyrus	brain
25	chr19:43001400-43003600	Enhancers	Stomach Mucosa	stomach
26	chr19:43001600-43002400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr19:43001600-43002800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr19:43001600-43003000	Flanking Active TSS	A549	lung
29	chr19:43001600-43003200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr19:43001800-43002400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr19:43001800-43002400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr19:43001800-43002400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:43001800-43002800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:43001800-43002800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr19:43001800-43002800	Enhancers	Pancreas	Pancrea
36	chr19:43001800-43003400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr19:43001800-43003600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr19:43001800-43003600	Enhancers	Brain Angular Gyrus	brain
39	chr19:43001800-43003600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr19:43001800-43003600	Enhancers	Brain Substantia Nigra	brain
41	chr19:43001800-43003600	Enhancers	Colonic Mucosa	Colon
42	chr19:43001800-43009400	Weak transcription	Aorta	Aorta
43	chr19:43002000-43002400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr19:43002000-43002400	Enhancers	Psoas Muscle	Psoas
45	chr19:43002000-43002600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:43002000-43002600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:43002000-43002600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr19:43002000-43002800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:43002000-43002800	Flanking Active TSS	Liver	Liver
50	chr19:43002000-43002800	Enhancers	Gastric	stomach

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