Variant report

Variant	rs480656
Chromosome Location	chr19:39925461-39925462
allele	C/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	chr19:39920860-39927633	U87	brain:	n/a	n/a
2	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
5	CHD1	chr19:39924942-39925688	GM12878	blood:	n/a	n/a
6	CHD1	chr19:39922434-39927571	IMR90	lung:	n/a	chr19:39927410-39927420
7	POLR2A	chr19:39920942-39925617	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:39920975-39927064	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39920712-39925660	IMR90	lung:	n/a	n/a
11	BCL3	chr19:39922482-39925602	A549	lung:	n/a	chr19:39924869-39924878
12	POLR2A	chr19:39921015-39927381	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:39921127-39925489	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:39922588-39925489	HL-60	blood:	n/a	n/a
15	POLR2A	chr19:39922723-39925532	K562	blood:	n/a	n/a
16	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
17	POLR2A	chr19:39920992-39925485	GM12891	blood:	n/a	n/a
18	SIN3AK20	chr19:39924841-39925791	A549	lung:	n/a	n/a
19	POLR2A	chr19:39921169-39925654	K562	blood:	n/a	n/a
20	REST	chr19:39924805-39925732	A549	lung:	n/a	chr19:39924867-39924880
21	MYC	chr19:39924499-39927878	A549	lung:	n/a	n/a
22	POLR2A	chr19:39921059-39925766	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
24	FOSL2	chr19:39925433-39927501	A549	lung:	n/a	chr19:39927413-39927422
25	SIN3AK20	chr19:39924641-39925466	A549	lung:	n/a	n/a
26	POLR2A	chr19:39921143-39925465	GM12878	blood:	n/a	n/a
27	MXI1	chr19:39924807-39925507	K562	blood:	n/a	n/a
28	EP300	chr19:39924067-39927364	A549	lung:	n/a	chr19:39925993-39926009 chr19:39927161-39927175
29	SIN3AK20	chr19:39920798-39927887	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr19:39920903-39927409	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr19:39920869-39927284	PFSK-1	brain:	n/a	n/a
32	REST	chr19:39924537-39925800	A549	lung:	n/a	chr19:39924867-39924880
33	POLR2A	chr19:39922546-39925580	HL-60	blood:	n/a	n/a
34	ETS1	chr19:39924145-39925749	A549	lung:	n/a	n/a
35	POLR2A	chr19:39925452-39925808	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:39921047-39927386	GM12892	blood:	n/a	n/a
37	POLR2A	chr19:39925210-39925504	MCF-7	breast:	n/a	n/a
38	POLR2A	chr19:39925141-39927033	K562	blood:	n/a	n/a
39	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
40	BCL3	chr19:39922499-39927500	A549	lung:	n/a	chr19:39926713-39926722 chr19:39927161-39927170 chr19:39926564-39926577 chr19:39925991-39926000 chr19:39924869-39924878
41	POLR2A	chr19:39921176-39925804	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr19:39920886-39928028	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr19:39920434-39927060	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:39922764-39925461	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:39921020-39925814	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:39924071-39925482	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:39920980-39927382	MCF10A-Er-Src	breast:	n/a	n/a
48	HEY1	chr19:39922803-39925717	K562	blood:	n/a	n/a
49	SP1	chr19:39925080-39927318	A549	lung:	n/a	chr19:39925991-39926000 chr19:39926456-39926465 chr19:39926689-39926698 chr19:39926687-39926699 chr19:39926455-39926469 chr19:39925992-39926001
50	POLR2A	chr19:39921288-39925465	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
2	chr19:39925083..39926660-chr19:39982191..39985073,2	K562	blood:
3	chr12:53661512..53662139-chr19:39925029..39925600,2	Hela-S3	cervix:
4	chr19:39924275..39926732-chr19:39958030..39960191,3	K562	blood:
5	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
6	chr19:39875302..39877706-chr19:39923653..39926638,3	MCF-7	breast:
7	chr19:39925059..39926909-chr6:27114877..27117589,2	MCF-7	breast:
8	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
9	chr19:39925068..39927999-chr19:40329043..40331985,2	K562	blood:
10	chr19:39832183..39834517-chr19:39925160..39926923,2	MCF-7	breast:
11	chr19:39925314..39927864-chr19:40336547..40338108,2	K562	blood:
12	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:
13	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
14	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
15	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:
16	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
17	chr19:39925075..39926642-chr19:40022135..40025107,3	K562	blood:

Variant related genes	Relation type
RPS16	TF binding region
SUPT5H	TF binding region
ENSG00000213922	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000135476	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1130180	0.81[ASN][1000 genomes]
rs11881477	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978920	0.83[ASN][1000 genomes]
rs1529732	0.81[ASN][1000 genomes]
rs17626	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865091	0.87[ASN][1000 genomes]
rs1865092	0.83[ASN][1000 genomes]
rs1932	0.84[ASN][1000 genomes]
rs2116932	0.84[ASN][1000 genomes]
rs2353678	0.87[ASN][1000 genomes]
rs2353679	0.86[ASN][1000 genomes]
rs251855	0.87[ASN][1000 genomes]
rs251856	0.89[ASN][1000 genomes]
rs251857	0.89[ASN][1000 genomes]
rs251858	0.89[ASN][1000 genomes]
rs251859	0.88[ASN][1000 genomes]
rs251860	0.85[ASN][1000 genomes]
rs28528765	0.83[ASN][1000 genomes]
rs28649498	0.82[ASN][1000 genomes]
rs4390710	0.87[ASN][1000 genomes]
rs4802026	0.83[ASN][1000 genomes]
rs4803237	0.81[ASN][1000 genomes]
rs480595	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481421	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504017	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs530411	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566130	0.91[ASN][1000 genomes]
rs640000	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508862	0.84[ASN][1000 genomes]
rs651601	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686956	0.89[ASN][1000 genomes]
rs7255253	0.81[ASN][1000 genomes]
rs73035416	0.81[ASN][1000 genomes]
rs73549933	0.81[ASN][1000 genomes]
rs8107194	0.81[ASN][1000 genomes]
rs8107647	0.81[ASN][1000 genomes]
rs8110134	0.85[ASN][1000 genomes]
rs8110716	0.85[ASN][1000 genomes]
rs878754	0.81[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs480656	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs480656	LOC441876///RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs480656	RPS16	cis	Muscle Skeletal	GTEx
rs480656	RPS16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39921600-39925600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39923200-39926200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr19:39923400-39925600	Transcr. at gene 5' and 3'	Hela-S3	cervix
5	chr19:39923600-39925600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr19:39923600-39926600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:39923800-39925600	Genic enhancers	Esophagus	oesophagus
8	chr19:39923800-39926400	Transcr. at gene 5' and 3'	A549	lung
9	chr19:39924000-39925600	Genic enhancers	Brain Anterior Caudate	brain
10	chr19:39924200-39925600	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr19:39924200-39925600	Genic enhancers	Brain Angular Gyrus	brain
12	chr19:39924200-39925600	Genic enhancers	Colon Smooth Muscle	Colon
13	chr19:39924200-39925600	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr19:39924200-39925600	Genic enhancers	Fetal Muscle Leg	muscle
15	chr19:39924200-39925600	Genic enhancers	Pancreas	Pancrea
16	chr19:39924200-39925600	Transcr. at gene 5' and 3'	NHLF	lung
17	chr19:39924200-39925800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
18	chr19:39924200-39926400	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr19:39924400-39925600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
20	chr19:39924400-39925600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr19:39924400-39925600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:39924400-39925600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
23	chr19:39924400-39925600	Genic enhancers	Placenta	Placenta
24	chr19:39924400-39925600	Genic enhancers	Fetal Thymus	thymus
25	chr19:39924400-39925600	Transcr. at gene 5' and 3'	K562	blood
26	chr19:39924400-39925800	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr19:39924600-39925600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
28	chr19:39924600-39925600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr19:39924600-39925600	Genic enhancers	Liver	Liver
30	chr19:39924600-39925600	Genic enhancers	Fetal Stomach	stomach
31	chr19:39924600-39925600	Transcr. at gene 5' and 3'	NH-A	brain
32	chr19:39924600-39925800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
33	chr19:39924600-39925800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39924600-39925800	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
35	chr19:39924600-39926000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:39924600-39926200	Transcr. at gene 5' and 3'	NHEK	skin
37	chr19:39924600-39926400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
38	chr19:39924800-39925600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
39	chr19:39924800-39925600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:39924800-39925600	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr19:39924800-39925800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39924800-39925800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
43	chr19:39924800-39925800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
44	chr19:39925000-39925600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:39925000-39925600	Transcr. at gene 5' and 3'	Fetal Lung	lung
46	chr19:39925000-39925800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:39925000-39925800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:39925000-39925800	Enhancers	Right Atrium	heart
49	chr19:39925000-39926000	Enhancers	Small Intestine	intestine
50	chr19:39925000-39926600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood

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