Variant report

Variant	rs12609354
Chromosome Location	chr19:38772077-38772078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38759485..38762494-chr19:38770790..38773902,4	K562	blood:
2	chr19:38770173..38772306-chr19:38806423..38808075,2	K562	blood:
3	chr19:38770260..38772183-chr19:38775620..38777576,2	K562	blood:

Variant related genes	Relation type
ENSG00000167645	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12610791	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12975244	0.83[ASN][1000 genomes]
rs12983492	0.83[ASN][1000 genomes]
rs2060244	0.90[AMR][1000 genomes]
rs2302227	1.00[AFR][1000 genomes]
rs34992016	0.86[AMR][1000 genomes]
rs3745949	0.90[AMR][1000 genomes]
rs6508782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12609354	MAP4K1	cis	thalamus	BrainEAC

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38756600-38772600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:38756600-38772600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38756800-38772600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr19:38756800-38774800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:38756800-38775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:38756800-38778600	Weak transcription	Thymus	Thymus
7	chr19:38756800-38779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:38758000-38774200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr19:38758400-38774400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:38759600-38783200	Weak transcription	Fetal Brain Male	brain
11	chr19:38761600-38773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:38765800-38772400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
14	chr19:38768800-38772600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:38769200-38772800	Weak transcription	Fetal Thymus	thymus
16	chr19:38769200-38773800	Weak transcription	Stomach Mucosa	stomach
17	chr19:38769200-38774400	Genic enhancers	HMEC	breast
18	chr19:38769200-38774800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:38769200-38778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:38769200-38791200	Weak transcription	Fetal Kidney	kidney
21	chr19:38769400-38772800	Weak transcription	Ovary	ovary
22	chr19:38769400-38776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:38769400-38779200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:38769600-38775200	Weak transcription	NHDF-Ad	bronchial
26	chr19:38769600-38778400	Weak transcription	Brain Substantia Nigra	brain
27	chr19:38769800-38772600	Weak transcription	HSMMtube	muscle
28	chr19:38769800-38773000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:38769800-38775600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:38769800-38775800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:38769800-38778000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:38769800-38778200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38769800-38778200	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:38769800-38779000	Weak transcription	Brain Anterior Caudate	brain
35	chr19:38769800-38779000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:38769800-38779000	Weak transcription	HSMM	muscle
37	chr19:38769800-38779200	Weak transcription	Brain Angular Gyrus	brain
38	chr19:38769800-38780400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:38770000-38774000	Weak transcription	HUVEC	blood vessel
40	chr19:38770000-38780600	Weak transcription	Brain Germinal Matrix	brain
41	chr19:38770400-38773200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:38770400-38774200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:38770400-38774400	Genic enhancers	NHEK	skin
44	chr19:38770600-38772200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:38770600-38777000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:38770800-38773200	Strong transcription	Primary B cells from cord blood	blood
47	chr19:38770800-38773400	Genic enhancers	A549	lung
48	chr19:38770800-38775000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr19:38770800-38785800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:38771200-38774000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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