Variant report

Variant	rs7255253
Chromosome Location	chr19:39945835-39945836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr19:39945472-39945847	HL-60	blood:	n/a	n/a
2	POLR2A	chr19:39945242-39945969	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39944081..39946194-chr19:39971487..39974078,2	MCF-7	breast:

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10412931	0.85[EUR][1000 genomes]
rs10423537	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10424217	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110627	0.86[EUR][1000 genomes]
rs1130180	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609112	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978920	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978954	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12979605	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12983040	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1529732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560730	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17626	0.81[ASN][1000 genomes]
rs17628	0.81[ASN][1000 genomes]
rs1865091	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865092	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1932	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009970	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060270	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060271	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060272	0.87[EUR][1000 genomes]
rs2116932	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288933	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288934	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2304219	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304221	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353678	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353679	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs251855	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs251856	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs251857	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs251858	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs251859	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs251860	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28528765	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637729	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28649498	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31727	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs31728	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34918990	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35647910	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4390710	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802026	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803237	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803240	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803241	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803242	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803245	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803246	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803247	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803250	0.83[EUR][1000 genomes]
rs480595	0.81[ASN][1000 genomes]
rs480656	0.81[ASN][1000 genomes]
rs481421	0.81[ASN][1000 genomes]
rs504017	0.85[ASN][1000 genomes]
rs530411	0.83[ASN][1000 genomes]
rs566130	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59007555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640000	0.81[ASN][1000 genomes]
rs6508862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6508863	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508864	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508865	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs686956	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7251384	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251652	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73035416	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73549933	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107194	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107647	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110134	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110716	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111260	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs878754	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7255253	RPS16	cis	Heart Left Ventricle	GTEx
rs7255253	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39936800-39949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39937000-39949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
5	chr19:39937600-39946000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
7	chr19:39937800-39946200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:39938800-39946400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:39939000-39946000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:39939000-39950000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:39939000-39953400	Strong transcription	Fetal Intestine Small	intestine
13	chr19:39939200-39948800	Weak transcription	Stomach Mucosa	stomach
14	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
15	chr19:39939400-39946000	Strong transcription	Lung	lung
16	chr19:39939400-39946000	Strong transcription	NHEK	skin
17	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
18	chr19:39940000-39948000	Weak transcription	Psoas Muscle	Psoas
19	chr19:39940000-39950400	Weak transcription	Small Intestine	intestine
20	chr19:39940000-39952200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
26	chr19:39940400-39946200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:39940400-39949000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:39941000-39951800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:39941200-39949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:39941200-39952800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:39941200-39953200	Strong transcription	Dnd41	blood
32	chr19:39941200-39954200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:39941400-39952200	Strong transcription	Fetal Brain Female	brain
34	chr19:39941400-39967400	Strong transcription	Fetal Intestine Large	intestine
35	chr19:39941600-39947400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:39942000-39946200	Strong transcription	Primary T cells from cord blood	blood
37	chr19:39942000-39967400	Strong transcription	Thymus	Thymus
38	chr19:39942000-39967600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:39942200-39946000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:39942200-39946000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:39942200-39953200	Strong transcription	Brain Angular Gyrus	brain
42	chr19:39942200-39967600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:39942200-39967600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:39942200-39967600	Strong transcription	Placenta	Placenta
45	chr19:39942200-39967600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:39942200-39967800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:39942400-39946000	Strong transcription	HepG2	liver
48	chr19:39942400-39946000	Strong transcription	HMEC	breast
49	chr19:39942400-39952400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:39942400-39953400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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