Variant report

Variant	rs56183542
Chromosome Location	chr19:41136534-41136535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41058638..41061458-chr19:41134495..41136638,2	K562	blood:
2	chr19:41118449..41121335-chr19:41135713..41138287,4	K562	blood:

Variant related genes	Relation type
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10880	0.83[ASN][1000 genomes]
rs11670451	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610819	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162857	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278242	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28580028	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786529	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7367	0.91[EUR][1000 genomes];0.91[ASN][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56183542	SHKBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
7	chr19:41121200-41137400	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:41121400-41140200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:41121800-41136800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:41122000-41136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:41123000-41136800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:41123400-41140400	Weak transcription	Liver	Liver
13	chr19:41124200-41136600	Weak transcription	HSMMtube	muscle
14	chr19:41125200-41137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:41125800-41136600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:41126000-41139000	Weak transcription	NHDF-Ad	bronchial
17	chr19:41126000-41139800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:41126000-41140000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:41126200-41140200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:41127000-41137400	Strong transcription	Fetal Lung	lung
21	chr19:41127600-41138400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:41127600-41140200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:41128200-41140000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:41128800-41140200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:41130000-41136600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:41130000-41136600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:41130000-41136600	Weak transcription	Fetal Brain Female	brain
28	chr19:41130000-41137000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:41130000-41137000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:41130000-41138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:41130000-41140200	Weak transcription	Brain Germinal Matrix	brain
32	chr19:41130200-41136800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:41130200-41136800	Strong transcription	Fetal Stomach	stomach
34	chr19:41130200-41136800	Weak transcription	Pancreas	Pancrea
35	chr19:41130200-41138200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr19:41130200-41139000	Weak transcription	A549	lung
37	chr19:41130200-41139600	Weak transcription	HUVEC	blood vessel
38	chr19:41130200-41140200	Weak transcription	Right Atrium	heart
39	chr19:41130400-41140200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:41130800-41137000	Strong transcription	Fetal Intestine Large	intestine
41	chr19:41131200-41137400	Strong transcription	Fetal Intestine Small	intestine
42	chr19:41131400-41137000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:41131800-41140000	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:41132000-41136600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:41132200-41138400	Weak transcription	NH-A	brain
46	chr19:41132400-41136600	Weak transcription	Left Ventricle	heart
47	chr19:41132400-41136800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:41132400-41137200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:41132400-41137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr19:41132400-41139200	Weak transcription	Stomach Mucosa	stomach

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