Variant report

Variant	rs6508864
Chromosome Location	chr19:39977650-39977651
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	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39977567-39977681	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:39977451-39977844	K562	blood:	n/a	n/a
4	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
TIMM50	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10412931	0.91[EUR][1000 genomes]
rs10423537	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424217	0.88[EUR][1000 genomes]
rs1110627	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1130180	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12609112	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12978920	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12978954	0.82[EUR][1000 genomes]
rs12979605	0.81[EUR][1000 genomes]
rs12983040	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1529732	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560730	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1865091	0.88[EUR][1000 genomes]
rs1865092	0.91[EUR][1000 genomes]
rs1932	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2009970	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060270	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060271	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060272	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2116932	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288933	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288934	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304219	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304221	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353678	0.87[EUR][1000 genomes]
rs2353679	0.87[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	0.86[EUR][1000 genomes]
rs251860	0.83[EUR][1000 genomes]
rs28528765	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28620146	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28637729	0.85[EUR][1000 genomes]
rs28649498	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34918990	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35647910	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4390710	0.87[EUR][1000 genomes]
rs4802026	0.89[EUR][1000 genomes]
rs4802031	0.81[AMR][1000 genomes]
rs4803237	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803240	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803241	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803242	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803245	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803246	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803247	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803250	0.89[EUR][1000 genomes]
rs566130	0.87[EUR][1000 genomes]
rs59007555	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508862	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508863	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508865	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs686956	0.87[EUR][1000 genomes]
rs7251384	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251652	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7255253	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73035416	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73549933	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8107194	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8107647	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110134	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8110716	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8111260	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878754	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6508864	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr19:39972800-39978800	Weak transcription	NHDF-Ad	bronchial
3	chr19:39972800-39980200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:39972800-39982200	Weak transcription	Fetal Kidney	kidney
5	chr19:39972800-39983200	Strong transcription	Fetal Brain Female	brain
6	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
7	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
8	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
9	chr19:39973000-39981600	Strong transcription	NHEK	skin
10	chr19:39973000-39982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:39973000-39983000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:39973000-39983000	Strong transcription	Fetal Intestine Small	intestine
13	chr19:39973000-39983800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:39973200-39983800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:39973200-39983800	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:39973400-39979600	Strong transcription	HSMM	muscle
17	chr19:39973400-39981400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:39973400-39981400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr19:39973400-39981400	Strong transcription	Fetal Intestine Large	intestine
20	chr19:39973400-39982400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:39973400-39982800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:39973400-39983000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:39973400-39983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:39973400-39983000	Strong transcription	Thymus	Thymus
25	chr19:39973400-39983200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:39973400-39983200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:39973400-39983200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:39973400-39983200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39973400-39983200	Strong transcription	Primary T cells from cord blood	blood
30	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:39973400-39983400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:39973400-39983800	Strong transcription	Brain Germinal Matrix	brain
34	chr19:39973600-39980800	Strong transcription	K562	blood
35	chr19:39973600-39981200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:39973600-39981400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr19:39973600-39981400	Strong transcription	Fetal Lung	lung
38	chr19:39973600-39981400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:39973600-39982000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:39973600-39982800	Strong transcription	Adipose Nuclei	Adipose
41	chr19:39973600-39983000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr19:39973600-39983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:39973600-39983200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:39973600-39983200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:39973600-39983200	Strong transcription	Liver	Liver
46	chr19:39973600-39983200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
48	chr19:39973800-39980000	Strong transcription	A549	lung
49	chr19:39973800-39981400	Strong transcription	Brain Angular Gyrus	brain
50	chr19:39973800-39983200	Strong transcription	Rectal Mucosa Donor 29	rectum

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