Variant report

Variant	rs10423371
Chromosome Location	chr19:52864251-52864252
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52861080..52862902-chr19:52863243..52865852,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10401299	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406085	1.00[ASW][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412822	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418954	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420125	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423818	1.00[AMR][1000 genomes]
rs10424465	1.00[AFR][1000 genomes]
rs2560886	1.00[ASW][hapmap];0.91[MKK][hapmap];0.85[AFR][1000 genomes]
rs2560986	0.85[AFR][1000 genomes]
rs60323875	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73581108	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73581129	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic 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	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10423371	T	trans	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
7	chr19:52857600-52865200	Strong transcription	Brain Hippocampus Middle	brain
8	chr19:52858400-52866800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:52858800-52871800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:52859600-52865200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:52859600-52866000	Strong transcription	Dnd41	blood
12	chr19:52859600-52868800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:52859800-52865000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:52859800-52866800	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:52859800-52868200	Weak transcription	Right Ventricle	heart
16	chr19:52860400-52864400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:52860600-52864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:52860600-52865200	Weak transcription	Placenta	Placenta
19	chr19:52861800-52864400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:52861800-52872200	ZNF genes & repeats	Fetal Lung	lung
21	chr19:52862000-52866800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:52862000-52870200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr19:52862000-52871000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr19:52862000-52871000	ZNF genes & repeats	Fetal Brain Female	brain
25	chr19:52862000-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:52862200-52864400	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr19:52862600-52864600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr19:52862600-52865400	ZNF genes & repeats	Left Ventricle	heart
29	chr19:52862600-52871400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:52862800-52865800	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr19:52862800-52870600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr19:52863000-52865200	Weak transcription	Fetal Kidney	kidney
33	chr19:52863000-52865800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:52863000-52868600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:52863200-52865200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:52863200-52866400	Weak transcription	Gastric	stomach
37	chr19:52863400-52867000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:52863600-52864600	Weak transcription	Aorta	Aorta
39	chr19:52863600-52864600	Weak transcription	Fetal Stomach	stomach
40	chr19:52863600-52864600	Weak transcription	Lung	lung
41	chr19:52863600-52865200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:52863600-52865200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:52863600-52866600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:52863600-52866800	Weak transcription	Brain Anterior Caudate	brain
45	chr19:52863600-52867000	Weak transcription	HSMMtube	muscle
46	chr19:52864000-52867800	Weak transcription	Fetal Brain Male	brain
47	chr19:52864200-52865200	Weak transcription	Fetal Muscle Leg	muscle
48	chr19:52864200-52865400	Weak transcription	Psoas Muscle	Psoas
49	chr19:52864200-52865800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:52864200-52866600	Weak transcription	Brain Angular Gyrus	brain

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