Variant report

Variant	rs2385005
Chromosome Location	chr19:38192892-38192893
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10445548	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061753	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061756	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150862	0.91[ASN][1000 genomes]
rs12151082	0.91[ASN][1000 genomes]
rs12151156	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244713	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244769	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17248097	0.91[ASN][1000 genomes]
rs17248670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17249138	0.91[ASN][1000 genomes]
rs17303902	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17304703	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305193	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305228	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17305823	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17306900	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1871196	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291001	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306201	0.96[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.96[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4536583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55681348	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55718806	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55743020	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754546	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865869	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909413	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56184201	0.91[ASN][1000 genomes]
rs56233644	0.91[ASN][1000 genomes]
rs56268127	0.91[ASN][1000 genomes]
rs56277404	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56290614	0.91[ASN][1000 genomes]
rs56351266	1.00[ASN][1000 genomes]
rs57654288	0.92[EUR][1000 genomes]
rs57943942	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7245855	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7259272	0.88[CEU][hapmap]
rs73031330	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033122	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033134	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73033142	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73035159	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73035160	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041006	1.00[ASN][1000 genomes]
rs73041036	0.91[ASN][1000 genomes]
rs7343065	1.00[CHB][hapmap]
rs8101610	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104282	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104994	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108268	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110293	0.91[ASN][1000 genomes]
rs8111790	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	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
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2385005	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs2385005	ZNF781	cis	Thyroid	GTEx
rs2385005	AC012309.5	cis	Thyroid	GTEx
rs2385005	AC012309.5	cis	Esophagus Mucosa	GTEx
rs2385005	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2385005	AC012309.5	cis	lung	GTEx
rs2385005	ZNF781	cis	Adipose Subcutaneous	GTEx
rs2385005	AC012309.5	cis	Esophagus Muscularis	GTEx
rs2385005	AC012309.5	cis	Artery Tibial	GTEx
rs2385005	AC012309.5	cis	Muscle Skeletal	GTEx
rs2385005	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
3	chr19:38184400-38208800	Weak transcription	HepG2	liver
4	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38187400-38199000	ZNF genes & repeats	A549	lung
7	chr19:38187400-38205800	Strong transcription	Dnd41	blood
8	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38188000-38198200	Weak transcription	Pancreas	Pancrea
10	chr19:38188200-38197800	Weak transcription	Right Ventricle	heart
11	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38188400-38195600	Weak transcription	Fetal Intestine Small	intestine
13	chr19:38188400-38202000	Weak transcription	Placenta	Placenta
14	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:38189800-38195600	Weak transcription	Fetal Stomach	stomach
16	chr19:38190000-38193600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:38190400-38196200	Weak transcription	Spleen	Spleen
19	chr19:38190400-38196800	Weak transcription	Gastric	stomach
20	chr19:38190400-38197200	Weak transcription	Small Intestine	intestine
21	chr19:38190600-38194200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:38190600-38194400	Weak transcription	NHDF-Ad	bronchial
23	chr19:38190600-38194600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:38190600-38196200	Weak transcription	Fetal Brain Female	brain
25	chr19:38190600-38196800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:38190600-38197000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:38190600-38197200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:38190600-38197200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:38190600-38197200	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:38190600-38197200	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:38190600-38197400	Weak transcription	Thymus	Thymus
32	chr19:38190600-38198000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:38190600-38198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:38190600-38198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
36	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
37	chr19:38190800-38193400	Weak transcription	Hela-S3	cervix
38	chr19:38190800-38195800	Weak transcription	Brain Germinal Matrix	brain
39	chr19:38190800-38196000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:38190800-38196200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:38190800-38197200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:38190800-38197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:38190800-38197200	Weak transcription	Fetal Intestine Large	intestine
44	chr19:38190800-38197200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:38190800-38198200	Weak transcription	Brain Angular Gyrus	brain
46	chr19:38190800-38198200	Weak transcription	Osteobl	bone
47	chr19:38190800-38198600	Weak transcription	HSMM	muscle
48	chr19:38190800-38202200	Weak transcription	NH-A	brain
49	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
50	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus

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