Variant report

Variant	rs56044734
Chromosome Location	chr19:19366927-19366928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19365186..19369263-chr19:19370853..19375419,4	K562	blood:
2	chr19:19365186..19370293-chr19:19370853..19374199,4	K562	blood:
3	chr19:19334544..19336643-chr19:19365954..19367462,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NCAN-2	chr19:19366316-19367760	NONHSAT063038

Variant related genes	Relation type
ENSG00000187664	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10401714	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10403273	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10407933	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10422893	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10423874	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1064395	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11555053	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1557723	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16996008	1.00[ASN][1000 genomes]
rs17216041	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17751061	0.93[EUR][1000 genomes]
rs1989867	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2010506	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2011503	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2074302	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315023	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965190	0.82[EUR][1000 genomes]
rs2965195	0.81[AMR][1000 genomes]
rs35854118	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4239639	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808932	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808933	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808934	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808944	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55762233	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55765017	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55822665	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56135441	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144632	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56212061	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56278919	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57436187	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511027	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257875	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72999030	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72999059	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72999063	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999068	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs756999	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8100097	0.86[EUR][1000 genomes]
rs8108777	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs998732	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56044734	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19346000-19367000	Weak transcription	Brain Anterior Caudate	brain
2	chr19:19347400-19367200	Weak transcription	Fetal Brain Male	brain
3	chr19:19361600-19367400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:19361600-19367800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:19361600-19372200	Weak transcription	Brain Angular Gyrus	brain
6	chr19:19363200-19367000	Weak transcription	Fetal Brain Female	brain
7	chr19:19363400-19371600	Weak transcription	Brain Germinal Matrix	brain
8	chr19:19366400-19368200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:19366600-19367800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19366600-19367800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:19366600-19368200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19366600-19368200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr19:19366800-19367000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:19366800-19367200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:19366800-19367200	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr19:19366800-19367400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:19366800-19367400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr19:19366800-19367600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:19366800-19367600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:19366800-19367600	Enhancers	Cortex derived primary cultured neurospheres	brain

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