Variant report

Variant	rs1474061
Chromosome Location	chr19:44533789-44533790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44532064..44534600-chr19:44536249..44538917,3	K562	blood:
2	chr19:44533699..44535211-chr19:44554393..44556460,2	MCF-7	breast:
3	chr19:44528641..44530994-chr19:44532234..44535492,3	K562	blood:
4	chr19:44533100..44535646-chr19:44537417..44539730,2	K562	blood:

Variant related genes	Relation type
ENSG00000178386	Chromatin interaction
ENSG00000267144	Chromatin interaction
ENSG00000159885	Chromatin interaction
ENSG00000267022	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11083734	0.91[ASN][1000 genomes]
rs11083735	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083736	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083737	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666432	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610472	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996409	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138823	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138824	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176431	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35120085	0.81[ASN][1000 genomes]
rs382197	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826941	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4239528	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs427608	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4299256	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4371266	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4375771	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4444434	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs451388	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs454904	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4550576	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4555257	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803668	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803672	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803674	0.81[EUR][1000 genomes]
rs55798868	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56003307	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56230322	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56250154	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57895932	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62115491	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62119177	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509135	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509137	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6509139	0.81[EUR][1000 genomes]
rs7251015	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252213	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255192	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257809	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105003	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109313	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109615	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110348	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9646633	0.92[EUR][1000 genomes];0.90[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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1474061	ZNF223	cis	Thyroid	GTEx
rs1474061	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs1474061	ZNF223	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44530200-44535400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44530400-44536200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:44530600-44534400	Weak transcription	Stomach Mucosa	stomach
4	chr19:44530600-44534600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:44530600-44534800	Weak transcription	HUVEC	blood vessel
6	chr19:44530600-44535000	Weak transcription	HMEC	breast
7	chr19:44530800-44534200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:44530800-44534600	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr19:44530800-44534600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:44530800-44537000	ZNF genes & repeats	Fetal Kidney	kidney
11	chr19:44530800-44537000	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44530800-44537200	ZNF genes & repeats	Ovary	ovary
13	chr19:44530800-44539200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
14	chr19:44530800-44539600	ZNF genes & repeats	Fetal Brain Female	brain
15	chr19:44530800-44542600	ZNF genes & repeats	Liver	Liver
16	chr19:44531000-44533800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:44531000-44534000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:44531000-44534000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:44531000-44534200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:44531000-44534600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:44531000-44534600	Strong transcription	Fetal Brain Male	brain
22	chr19:44531000-44534600	Strong transcription	HSMM	muscle
23	chr19:44531000-44534800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:44531000-44534800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:44531000-44535000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr19:44531000-44535000	Strong transcription	HSMMtube	muscle
27	chr19:44531000-44535000	Strong transcription	Osteobl	bone
28	chr19:44531000-44535800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:44531000-44536400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:44531000-44537000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:44531000-44537000	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr19:44531000-44537000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:44531000-44537000	ZNF genes & repeats	Aorta	Aorta
34	chr19:44531000-44537000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
35	chr19:44531000-44537000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
36	chr19:44531000-44537000	ZNF genes & repeats	Thymus	Thymus
37	chr19:44531000-44537200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:44531000-44537200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:44531000-44537200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr19:44531000-44538000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:44531000-44538200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr19:44531000-44538200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:44531000-44538400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:44531000-44539400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr19:44531000-44540000	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr19:44531200-44533800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:44531200-44533800	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr19:44531200-44533800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr19:44531200-44534200	Strong transcription	Right Ventricle	heart
50	chr19:44531200-44534400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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