Variant report

Variant	rs2650810
Chromosome Location	chr19:21595732-21595733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-2	chr19:21594742-21597401	NONHSAT063703

Extended variants
information (count: 139 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10405716	0.86[ASN][1000 genomes]
rs1055753	0.86[ASN][1000 genomes]
rs10854043	0.82[ASN][1000 genomes]
rs11085443	0.81[ASN][1000 genomes]
rs11085447	0.85[ASN][1000 genomes]
rs1142653	0.83[ASN][1000 genomes]
rs11667770	0.86[ASN][1000 genomes]
rs11668691	0.86[ASN][1000 genomes]
rs11673304	0.82[ASN][1000 genomes]
rs11673406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12151067	0.84[EUR][1000 genomes]
rs12151068	0.84[EUR][1000 genomes]
rs12971736	0.81[ASN][1000 genomes]
rs12972580	0.83[ASN][1000 genomes]
rs12974735	0.82[ASN][1000 genomes]
rs12975081	0.83[ASN][1000 genomes]
rs12975464	0.82[ASN][1000 genomes]
rs12975981	0.83[EUR][1000 genomes]
rs12979646	0.86[ASN][1000 genomes]
rs12981564	0.83[ASN][1000 genomes]
rs12981735	0.83[ASN][1000 genomes]
rs12981775	0.83[ASN][1000 genomes]
rs12981869	0.82[EUR][1000 genomes]
rs12982162	0.83[ASN][1000 genomes]
rs12982282	0.83[ASN][1000 genomes]
rs12983787	0.86[ASN][1000 genomes]
rs12984871	0.83[ASN][1000 genomes]
rs17618778	0.81[EUR][1000 genomes]
rs1813234	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1963531	0.81[ASN][1000 genomes]
rs1963532	0.82[ASN][1000 genomes]
rs1976384	0.86[ASN][1000 genomes]
rs2012013	0.82[ASN][1000 genomes]
rs2012038	0.82[ASN][1000 genomes]
rs2061917	0.82[ASN][1000 genomes]
rs2061918	0.81[ASN][1000 genomes]
rs2061919	0.81[ASN][1000 genomes]
rs2086318	0.80[ASN][1000 genomes]
rs2086320	0.85[ASN][1000 genomes]
rs2088762	0.83[ASN][1000 genomes]
rs2102072	0.85[ASN][1000 genomes]
rs2127404	0.83[ASN][1000 genomes]
rs2127405	0.83[ASN][1000 genomes]
rs2127406	0.83[ASN][1000 genomes]
rs2127407	0.83[ASN][1000 genomes]
rs2127408	0.83[ASN][1000 genomes]
rs2170024	0.85[ASN][1000 genomes]
rs2170025	0.85[ASN][1000 genomes]
rs2173728	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2219840	0.83[ASN][1000 genomes]
rs2262896	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358984	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2358985	0.80[ASN][1000 genomes]
rs2358986	0.83[ASN][1000 genomes]
rs2358988	0.83[ASN][1000 genomes]
rs2358989	0.84[ASN][1000 genomes]
rs2358990	0.83[ASN][1000 genomes]
rs2358991	0.85[ASN][1000 genomes]
rs2358992	0.85[ASN][1000 genomes]
rs2434997	0.85[ASN][1000 genomes]
rs2454920	0.83[AFR][1000 genomes]
rs2650775	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2650847	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28839521	0.82[EUR][1000 genomes]
rs2884601	0.80[ASN][1000 genomes]
rs2914629	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914638	0.85[ASN][1000 genomes]
rs2928208	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2937161	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34560125	0.84[EUR][1000 genomes]
rs34875588	0.81[EUR][1000 genomes]
rs35148123	0.81[EUR][1000 genomes]
rs35578515	0.82[EUR][1000 genomes]
rs35773446	0.86[ASN][1000 genomes]
rs35829872	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35860067	0.81[EUR][1000 genomes]
rs4315457	0.83[ASN][1000 genomes]
rs4341872	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4438422	0.84[ASN][1000 genomes]
rs4461198	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56080558	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110379	0.82[EUR][1000 genomes]
rs6511228	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6511229	0.81[ASN][1000 genomes]
rs6511231	0.83[ASN][1000 genomes]
rs6511232	0.83[ASN][1000 genomes]
rs6511233	0.83[ASN][1000 genomes]
rs6511237	0.82[ASN][1000 genomes]
rs6511238	0.86[ASN][1000 genomes]
rs6511239	0.86[ASN][1000 genomes]
rs6511242	0.86[ASN][1000 genomes]
rs6511245	0.86[ASN][1000 genomes]
rs6511246	0.86[ASN][1000 genomes]
rs67723811	0.84[EUR][1000 genomes]
rs7245920	0.83[ASN][1000 genomes]
rs7246684	0.82[EUR][1000 genomes]
rs7247411	0.85[ASN][1000 genomes]
rs7248601	0.86[ASN][1000 genomes]
rs7249412	0.86[ASN][1000 genomes]
rs7252873	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7254059	0.86[ASN][1000 genomes]
rs7257580	0.85[ASN][1000 genomes]
rs7257857	0.85[ASN][1000 genomes]
rs7258086	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7258335	0.83[ASN][1000 genomes]
rs7259311	0.86[ASN][1000 genomes]
rs7508092	0.81[ASN][1000 genomes]
rs7508671	0.83[ASN][1000 genomes]
rs8099940	0.83[ASN][1000 genomes]
rs8102328	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8102342	0.82[ASN][1000 genomes]
rs8103325	0.83[ASN][1000 genomes]
rs8103459	0.83[ASN][1000 genomes]
rs8103908	0.83[ASN][1000 genomes]
rs8104017	0.82[ASN][1000 genomes]
rs8105404	0.82[EUR][1000 genomes]
rs8106936	0.84[ASN][1000 genomes]
rs8110230	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8110690	0.83[ASN][1000 genomes]
rs8110967	0.80[ASN][1000 genomes]
rs8112583	0.83[ASN][1000 genomes]
rs8113558	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
16	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2650810	ZNF429	cis	Adipose Subcutaneous	GTEx
rs2650810	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs2650810	ZNF429	cis	Whole Blood	GTEx
rs2650810	ZNF738	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21600200	Weak transcription	Gastric	stomach
2	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21581000-21596200	Weak transcription	Aorta	Aorta
4	chr19:21581000-21598800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21581400-21596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:21581400-21598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:21583800-21596200	Weak transcription	Brain Substantia Nigra	brain
10	chr19:21583800-21598200	Weak transcription	Fetal Brain Male	brain
11	chr19:21584000-21596200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:21584000-21596200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:21584000-21597400	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:21584800-21598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:21585000-21596800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:21586000-21599400	Weak transcription	Spleen	Spleen
18	chr19:21586600-21596200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:21586800-21598400	Weak transcription	Colonic Mucosa	Colon
20	chr19:21588200-21598600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:21588400-21596600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:21588400-21597600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:21588600-21596600	Strong transcription	Fetal Stomach	stomach
24	chr19:21588800-21596200	Weak transcription	Fetal Thymus	thymus
25	chr19:21589600-21598200	Weak transcription	NHDF-Ad	bronchial
26	chr19:21590000-21600200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr19:21590600-21598400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:21590600-21598600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:21590800-21595800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:21590800-21601200	Strong transcription	Ovary	ovary
33	chr19:21591200-21597000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:21591600-21599000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:21591800-21597200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
37	chr19:21592000-21597600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:21592200-21596800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:21592200-21597200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr19:21592200-21597600	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:21592200-21597800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr19:21592400-21597400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:21592400-21598600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
44	chr19:21592600-21596000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:21592600-21596200	Weak transcription	Right Ventricle	heart
46	chr19:21592600-21598200	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:21592800-21596200	Weak transcription	Brain Anterior Caudate	brain
48	chr19:21592800-21596200	Weak transcription	NH-A	brain
49	chr19:21592800-21601200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:21593200-21602400	Weak transcription	HSMM	muscle

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