Variant report

Variant	rs6508862
Chromosome Location	chr19:39935342-39935343
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	chr19:39935225-39935558	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr19:39935266-39936619	HUVEC	blood vessel:	n/a	n/a
3	REST	chr19:39935115-39937132	A549	lung:	n/a	chr19:39936465-39936478
4	HCFC1	chr19:39935163-39937047	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:39935211-39935663	U87	brain:	n/a	n/a
6	MXI1	chr19:39935156-39937409	IMR90	lung:	n/a	n/a
7	POLR2A	chr19:39935185-39936535	MCF10A-Er-Src	breast:	n/a	n/a
8	REST	chr19:39935219-39936867	H1-neurons	neurons:	n/a	chr19:39936465-39936478
9	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39935240-39936734	HUVEC	blood vessel:	n/a	n/a
11	E2F6	chr19:39935163-39936750	A549	lung:	n/a	n/a
12	ZBTB33	chr19:39935188-39936975	A549	lung:	n/a	chr19:39936192-39936207 chr19:39936195-39936205 chr19:39936197-39936206
13	POLR2A	chr19:39935279-39935356	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:39935238-39936522	MCF10A-Er-Src	breast:	n/a	n/a
15	BCL3	chr19:39935250-39936808	A549	lung:	n/a	chr19:39936443-39936456 chr19:39936410-39936419
16	SP1	chr19:39935291-39936739	A549	lung:	n/a	n/a
17	POLR2A	chr19:39935187-39936832	GM12878	blood:	n/a	n/a
18	ZNF384	chr19:39935119-39936334	K562	blood:	n/a	chr19:39936049-39936057
19	POLR2A	chr19:39935320-39936543	U87	brain:	n/a	n/a
20	CEBPB	chr19:39935180-39935377	K562	blood:	n/a	n/a
21	POLR2A	chr19:39935291-39936639	IMR90	lung:	n/a	n/a
22	SIN3AK20	chr19:39934802-39939537	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr19:39935214-39936711	HepG2	liver:	n/a	n/a
24	TCF7L2	chr19:39935313-39936761	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
26	YY1	chr19:39935194-39936784	A549	lung:	n/a	chr19:39936123-39936133 chr19:39936122-39936130 chr19:39936118-39936134 chr19:39936086-39936100 chr19:39936111-39936133
27	REST	chr19:39934933-39936825	PANC-1	pancreas:	n/a	chr19:39936465-39936478
28	POLR2A	chr19:39935209-39935525	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:39935207-39936747	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:39935206-39935509	GM12878	blood:	n/a	n/a
31	BCL3	chr19:39935141-39936780	A549	lung:	n/a	chr19:39936443-39936456 chr19:39936410-39936419
32	YY1	chr19:39935267-39936730	GM12878	blood:	n/a	chr19:39936123-39936133 chr19:39936122-39936130 chr19:39936118-39936134 chr19:39936086-39936100 chr19:39936111-39936133
33	ETS1	chr19:39935323-39936770	A549	lung:	n/a	chr19:39936197-39936206 chr19:39936407-39936420 chr19:39936410-39936421 chr19:39936164-39936173 chr19:39936411-39936421
34	GATA3	chr19:39935252-39936869	A549	lung:	n/a	n/a
35	POLR2A	chr19:39935328-39936681	U87	brain:	n/a	n/a
36	POLR2A	chr19:39935171-39936715	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr19:39935285-39936867	GM12891	blood:	n/a	n/a
38	MTA3	chr19:39935253-39936913	GM12878	blood:	n/a	n/a
39	MAX	chr19:39935205-39936832	A549	lung:	n/a	n/a
40	CHD1	chr19:39935054-39937337	IMR90	lung:	n/a	chr19:39936197-39936206
41	TCF12	chr19:39935059-39936939	A549	lung:	n/a	n/a
42	POLR2A	chr19:39935213-39936859	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr19:39934881-39939523	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr19:39935036-39936735	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr19:39935186-39936861	GM12892	blood:	n/a	n/a
46	POLR2A	chr19:39934929-39936596	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr19:39935295-39936756	K562	blood:	n/a	n/a
48	MAX	chr19:39935103-39937272	A549	lung:	n/a	n/a
49	POLR2A	chr19:39935150-39935608	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39934417..39936200-chr19:40029570..40032204,2	MCF-7	breast:
2	chr19:39934545..39937545-chr19:40023023..40025430,4	MCF-7	breast:
3	chr19:39641788..39643713-chr19:39934290..39936014,2	MCF-7	breast:
4	chr19:39934091..39937114-chr19:39969895..39972879,3	K562	blood:
5	chr12:7053697..7055521-chr19:39934988..39936687,2	MCF-7	breast:
6	chr19:39921621..39923975-chr19:39932520..39935648,3	MCF-7	breast:
7	chr19:39934676..39937838-chr19:39970025..39973557,7	MCF-7	breast:
8	chr19:39934091..39937562-chr19:39970121..39972977,5	K562	blood:
9	chr19:39933642..39937454-chr19:40029470..40032868,6	MCF-7	breast:
10	chr19:39930372..39932549-chr19:39934536..39937097,4	K562	blood:
11	chr19:39934791..39938517-chr19:40022234..40026334,4	K562	blood:
12	chr19:39934619..39937838-chr19:39970480..39972998,6	MCF-7	breast:
13	chr19:39903188..39905724-chr19:39934407..39937965,7	MCF-7	breast:
14	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS16-1	chr19:39932509-39936109	NONHSAT066299

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000269792	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000176396	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10412931	0.84[EUR][1000 genomes]
rs10423537	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424217	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1110627	0.85[EUR][1000 genomes]
rs1130180	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12609112	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978920	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12978954	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12979605	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12983040	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1529732	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1560730	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17626	0.84[ASN][1000 genomes]
rs17628	0.84[ASN][1000 genomes]
rs1865091	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865092	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1932	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009970	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060270	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060271	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060272	0.85[EUR][1000 genomes]
rs2116932	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288933	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288934	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304219	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304221	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2353678	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353679	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs251855	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs251856	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs251857	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs251858	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs251859	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs251860	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28528765	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28637729	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28649498	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31727	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs31728	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34918990	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35647910	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4390710	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802026	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803237	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803240	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803241	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803242	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803245	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803246	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803247	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803250	0.81[EUR][1000 genomes]
rs480595	0.84[ASN][1000 genomes]
rs480656	0.84[ASN][1000 genomes]
rs481421	0.84[ASN][1000 genomes]
rs504017	0.84[ASN][1000 genomes]
rs530411	0.86[ASN][1000 genomes]
rs566130	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59007555	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs640000	0.84[ASN][1000 genomes]
rs6508863	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508864	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508865	0.89[EUR][1000 genomes]
rs651601	0.83[ASN][1000 genomes]
rs686956	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251384	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7251652	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255253	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73035416	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73549933	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107194	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107647	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110134	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110716	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111260	0.91[EUR][1000 genomes]
rs878754	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6508862	RPS16	cis	Heart Left Ventricle	GTEx
rs6508862	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39934800-39937000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:39934800-39937000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:39934800-39937000	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr19:39934800-39937000	Active TSS	A549	lung
5	chr19:39934800-39937200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:39935000-39935400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:39935000-39935400	Flanking Active TSS	Dnd41	blood
8	chr19:39935000-39935600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:39935000-39935600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:39935000-39935600	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr19:39935000-39936200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:39935000-39936400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:39935000-39936400	Active TSS	Brain Germinal Matrix	brain
14	chr19:39935000-39936600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:39935000-39936600	Active TSS	Fetal Brain Female	brain
16	chr19:39935000-39936800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:39935000-39936800	Active TSS	Muscle Satellite Cultured Cells	--
18	chr19:39935000-39936800	Active TSS	HMEC	breast
19	chr19:39935000-39936800	Active TSS	NHEK	skin
20	chr19:39935000-39937000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:39935000-39937000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:39935000-39937000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:39935000-39937000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:39935000-39937000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39935000-39937000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:39935000-39937000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:39935000-39937000	Active TSS	Psoas Muscle	Psoas
28	chr19:39935000-39937000	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:39935000-39937000	Active TSS	Right Ventricle	heart
30	chr19:39935000-39937200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39935000-39937400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:39935000-39937400	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr19:39935000-39937400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr19:39935000-39937400	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:39935000-39937600	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr19:39935200-39935400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr19:39935200-39935400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr19:39935200-39935400	Flanking Active TSS	Liver	Liver
39	chr19:39935200-39935400	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr19:39935200-39935400	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr19:39935200-39935400	Flanking Active TSS	Fetal Brain Male	brain
42	chr19:39935200-39935400	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr19:39935200-39935400	Flanking Active TSS	Fetal Stomach	stomach
44	chr19:39935200-39935400	Flanking Active TSS	Stomach Mucosa	stomach
45	chr19:39935200-39935400	Flanking Active TSS	NH-A	brain
46	chr19:39935200-39935600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr19:39935200-39935600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr19:39935200-39935600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr19:39935200-39935600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr19:39935200-39935600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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