Variant report

Variant	rs12609112
Chromosome Location	chr19:39940651-39940652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39940271..39942805-chr19:39948760..39951555,2	K562	blood:
2	chr19:39935874..39939809-chr19:39940244..39944491,6	K562	blood:
3	chr19:39939856..39941421-chr19:40009261..40011843,2	K562	blood:

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10412931	0.85[EUR][1000 genomes]
rs10423537	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10424217	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1110627	0.86[EUR][1000 genomes]
rs1130180	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978920	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12978954	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979605	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12983040	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1529732	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560730	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865091	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1865092	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1932	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009970	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060270	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060271	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060272	0.86[EUR][1000 genomes]
rs2116932	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288933	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2288934	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304219	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304221	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353678	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2353679	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs251855	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251856	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251857	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251858	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251859	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251860	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28528765	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28637729	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28649498	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31727	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs31728	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34918990	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35647910	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4390710	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802026	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803237	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803240	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803241	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803242	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803245	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803246	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803247	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803250	0.82[EUR][1000 genomes]
rs504017	0.81[ASN][1000 genomes]
rs530411	0.81[ASN][1000 genomes]
rs566130	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59007555	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508862	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508863	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508864	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508865	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs651601	0.81[ASN][1000 genomes]
rs686956	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251384	0.92[EUR][1000 genomes]
rs7251652	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73035416	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73549933	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107194	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107647	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110134	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110716	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111260	0.92[EUR][1000 genomes]
rs878754	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12609112	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	chr19:39937200-39941600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:39937200-39943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:39937400-39941200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:39937400-39942800	Weak transcription	Fetal Kidney	kidney
8	chr19:39937400-39944600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
10	chr19:39937600-39946000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
12	chr19:39937800-39941600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr19:39937800-39942200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:39937800-39943400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:39937800-39946200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:39938000-39941800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:39938000-39942200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:39938200-39942800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:39938400-39941400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:39938400-39941400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:39938600-39941200	Genic enhancers	Spleen	Spleen
22	chr19:39938600-39941600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:39938800-39941400	Genic enhancers	Fetal Brain Female	brain
25	chr19:39938800-39943800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:39938800-39946400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:39939000-39941400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr19:39939000-39942200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:39939000-39946000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:39939000-39950000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:39939000-39953400	Strong transcription	Fetal Intestine Small	intestine
32	chr19:39939200-39941600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr19:39939200-39941600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:39939200-39942000	Weak transcription	Thymus	Thymus
35	chr19:39939200-39942400	Weak transcription	Fetal Lung	lung
36	chr19:39939200-39948800	Weak transcription	Stomach Mucosa	stomach
37	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
38	chr19:39939400-39940800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:39939400-39940800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:39939400-39941000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:39939400-39941000	Weak transcription	Brain Substantia Nigra	brain
42	chr19:39939400-39941200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr19:39939400-39942400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:39939400-39942600	Weak transcription	Colonic Mucosa	Colon
45	chr19:39939400-39942600	Weak transcription	Ovary	ovary
46	chr19:39939400-39942800	Weak transcription	Aorta	Aorta
47	chr19:39939400-39943400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:39939400-39943600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr19:39939400-39943800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:39939400-39943800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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