Variant report

Variant	rs10424079
Chromosome Location	chr19:21589179-21589180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10410362	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs10414834	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666213	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666447	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666525	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666540	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11667103	0.83[EUR][1000 genomes]
rs11667361	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11669033	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669790	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670815	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670868	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11672583	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11673320	0.81[AMR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11880751	1.00[CHB][hapmap]
rs13346641	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621154	0.83[EUR][1000 genomes]
rs1626404	0.83[EUR][1000 genomes]
rs1645806	1.00[CHB][hapmap]
rs1762578	0.83[EUR][1000 genomes]
rs17680605	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1781867	0.83[EUR][1000 genomes]
rs1781872	0.83[EUR][1000 genomes]
rs1963057	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs1967182	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011379	1.00[CHB][hapmap]
rs2061916	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154302	0.81[EUR][1000 genomes]
rs2358993	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359144	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359145	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359147	1.00[YRI][hapmap]
rs2454922	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs2562405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562413	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562416	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562456	0.83[CEU][hapmap]
rs2650776	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650844	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650848	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2801860	1.00[CHB][hapmap]
rs2914644	0.89[YRI][hapmap]
rs2968031	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs3853837	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3853838	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4321312	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4327181	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4359573	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4544364	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4638726	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55756795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55875743	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55899865	0.83[EUR][1000 genomes]
rs57299552	0.83[EUR][1000 genomes]
rs58412280	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60173523	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61035285	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62107465	0.81[EUR][1000 genomes]
rs62107469	0.81[EUR][1000 genomes]
rs62107472	0.83[EUR][1000 genomes]
rs62107479	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107531	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62107536	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62107539	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107540	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107541	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109225	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109226	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109227	0.86[AMR][1000 genomes]
rs62109228	0.86[AMR][1000 genomes]
rs62109229	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62110367	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62110377	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110416	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110420	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110424	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110426	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110427	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62110428	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110429	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246339	0.83[EUR][1000 genomes]
rs7251135	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258099	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7258473	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7258562	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7260065	1.00[CHB][hapmap]
rs73537884	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv978789	chr19:21579953-21589286	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10424079	CTD-2561J22.5	cis	Thyroid	GTEx
rs10424079	RP11-678G14.2	cis	Whole Blood	GTEx
rs10424079	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21592600	Weak transcription	Placenta	Placenta
2	chr19:21580600-21593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21580600-21593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:21580600-21600200	Weak transcription	Gastric	stomach
5	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21580800-21595400	Weak transcription	HUVEC	blood vessel
7	chr19:21581000-21591800	Weak transcription	Pancreas	Pancrea
8	chr19:21581000-21596200	Weak transcription	Aorta	Aorta
9	chr19:21581000-21598800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:21581200-21590200	Weak transcription	NHLF	lung
11	chr19:21581400-21592000	Weak transcription	NH-A	brain
12	chr19:21581400-21594600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:21581400-21596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:21581400-21598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:21581600-21590000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:21581600-21591800	Weak transcription	Right Ventricle	heart
17	chr19:21581600-21592200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:21581600-21592400	Weak transcription	Brain Angular Gyrus	brain
19	chr19:21581600-21592400	Weak transcription	Fetal Kidney	kidney
20	chr19:21581600-21594600	Weak transcription	HepG2	liver
21	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:21582200-21590800	Weak transcription	Fetal Lung	lung
24	chr19:21583800-21589200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:21583800-21592200	Weak transcription	Brain Anterior Caudate	brain
26	chr19:21583800-21595600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr19:21583800-21596200	Weak transcription	Brain Substantia Nigra	brain
28	chr19:21583800-21598200	Weak transcription	Fetal Brain Male	brain
29	chr19:21584000-21591800	Weak transcription	Osteobl	bone
30	chr19:21584000-21592200	Weak transcription	HSMMtube	muscle
31	chr19:21584000-21596200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:21584000-21596200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:21584000-21597400	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:21584200-21589200	Strong transcription	Dnd41	blood
35	chr19:21584400-21592800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:21584800-21598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:21585000-21589400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr19:21585000-21589400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr19:21585000-21590800	Strong transcription	Fetal Intestine Large	intestine
40	chr19:21585000-21596800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:21585200-21589400	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr19:21585200-21589600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:21585200-21589800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:21585200-21592200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:21585200-21592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:21585200-21594200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:21585400-21592000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr19:21585800-21589800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:21585800-21591000	Strong transcription	Primary T cells fromperipheralblood	blood

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