Variant report

Variant	rs8111260
Chromosome Location	chr19:39982081-39982082
allele	A/G
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	POLR2A	chr19:39982026-39982427	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	SIN3AK20	chr19:39981974-39985585	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39982069-39982496	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:39982048-39982427	K562	blood:	n/a	n/a
6	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:39981995-39983346	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39974324..39976296-chr19:39980616..39983158,2	MCF-7	breast:
2	chr19:39930044..39931944-chr19:39980921..39983797,2	MCF-7	breast:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000213922	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10412931	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10423537	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10424217	0.87[EUR][1000 genomes]
rs1110627	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1130180	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12609112	0.92[EUR][1000 genomes]
rs12978920	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12978954	0.81[EUR][1000 genomes]
rs12979605	0.81[EUR][1000 genomes]
rs12983040	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1529732	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1560730	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1865091	0.87[EUR][1000 genomes]
rs1865092	0.91[EUR][1000 genomes]
rs1932	0.92[EUR][1000 genomes]
rs2009970	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060270	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060271	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060272	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2116932	0.92[EUR][1000 genomes]
rs2288933	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288934	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304219	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304221	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353678	0.86[EUR][1000 genomes]
rs2353679	0.86[EUR][1000 genomes]
rs251855	0.87[EUR][1000 genomes]
rs251856	0.86[EUR][1000 genomes]
rs251857	0.87[EUR][1000 genomes]
rs251858	0.87[EUR][1000 genomes]
rs251859	0.85[EUR][1000 genomes]
rs251860	0.83[EUR][1000 genomes]
rs28528765	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28620146	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28637729	0.84[EUR][1000 genomes]
rs28649498	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34918990	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35647910	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4390710	0.86[EUR][1000 genomes]
rs4802026	0.89[EUR][1000 genomes]
rs4803237	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4803240	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803241	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803242	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803245	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803246	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803250	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs566130	0.87[EUR][1000 genomes]
rs59007555	0.92[EUR][1000 genomes]
rs6508862	0.91[EUR][1000 genomes]
rs6508863	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508865	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686956	0.86[EUR][1000 genomes]
rs7251384	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251652	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255253	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73035416	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73549933	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8107194	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8107647	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8110134	0.91[EUR][1000 genomes]
rs8110716	0.91[EUR][1000 genomes]
rs878754	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8111260	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972800-39982200	Weak transcription	Fetal Kidney	kidney
3	chr19:39972800-39983200	Strong transcription	Fetal Brain Female	brain
4	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
5	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
6	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
7	chr19:39973000-39983000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:39973000-39983000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:39973000-39983800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:39973200-39983800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:39973200-39983800	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:39973400-39982400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39973400-39982800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:39973400-39983000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:39973400-39983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:39973400-39983000	Strong transcription	Thymus	Thymus
17	chr19:39973400-39983200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:39973400-39983200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:39973400-39983200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:39973400-39983200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:39973400-39983200	Strong transcription	Primary T cells from cord blood	blood
22	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:39973400-39983400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:39973400-39983800	Strong transcription	Brain Germinal Matrix	brain
26	chr19:39973600-39982800	Strong transcription	Adipose Nuclei	Adipose
27	chr19:39973600-39983000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr19:39973600-39983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:39973600-39983200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:39973600-39983200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:39973600-39983200	Strong transcription	Liver	Liver
32	chr19:39973600-39983200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
34	chr19:39973800-39983200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:39973800-39983800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:39974000-39983000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:39974000-39983200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:39974000-39983400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:39974200-39982200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr19:39974200-39982400	Strong transcription	Left Ventricle	heart
41	chr19:39974200-39983200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:39974400-39983200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:39975000-39983200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:39975000-39983200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:39975000-39983200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:39975400-39983000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:39975400-39983000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr19:39975400-39983000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr19:39975400-39983200	Strong transcription	Ovary	ovary
50	chr19:39975400-39983200	Strong transcription	Spleen	Spleen

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