Variant report

Variant	rs8106642
Chromosome Location	chr19:39972068-39972069
allele	G/T
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	chr19:39971072-39972241	H1-hESC	embryonic stem cell:	n/a	n/a
2	HCFC1	chr19:39970889-39972362	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39970896-39972437	GM12891	blood:	n/a	n/a
4	YY1	chr19:39971125-39972129	ECC-1	luminal epithelium:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
5	ETS1	chr19:39971002-39972169	A549	lung:	n/a	chr19:39971797-39971810 chr19:39972147-39972156 chr19:39971089-39971102
6	USF1	chr19:39971071-39972077	ECC-1	luminal epithelium:	n/a	n/a
7	YY1	chr19:39971053-39972178	GM12878	blood:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
8	CHD1	chr19:39971163-39972137	GM12878	blood:	n/a	n/a
9	FOSL2	chr19:39970895-39972340	A549	lung:	n/a	n/a
10	POLR2A	chr19:39970952-39972248	GM12892	blood:	n/a	n/a
11	MXI1	chr19:39970630-39972480	SK-N-SH	brain:	n/a	chr19:39971811-39971820 chr19:39971813-39971822
12	SIN3AK20	chr19:39970991-39972108	A549	lung:	n/a	n/a
13	MAX	chr19:39970953-39972144	HepG2	liver:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
14	POLR2A	chr19:39971097-39972074	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:39970359-39972524	K562	blood:	n/a	n/a
16	TAF1	chr19:39970999-39972112	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
18	TFAP2C	chr19:39970955-39972193	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:39970991-39972499	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:39971131-39972077	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr19:39970971-39972368	A549	lung:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
22	MYC	chr19:39970732-39973093	A549	lung:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
23	NR2F2	chr19:39970021-39972664	K562	blood:	n/a	n/a
24	SMARCB1	chr19:39971134-39972278	Hela-S3	cervix:	n/a	n/a
25	REST	chr19:39970980-39972088	A549	lung:	n/a	chr19:39971694-39971708
26	SIX5	chr19:39970755-39972586	A549	lung:	n/a	n/a
27	NFATC1	chr19:39971107-39972103	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:39971059-39972265	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr19:39971050-39972210	K562	blood:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
30	TAF1	chr19:39971098-39972124	ECC-1	luminal epithelium:	n/a	n/a
31	MXI1	chr19:39970547-39972313	IMR90	lung:	n/a	chr19:39971811-39971820 chr19:39971813-39971822
32	MAX	chr19:39970971-39972149	A549	lung:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
33	SIN3AK20	chr19:39970726-39972314	A549	lung:	n/a	n/a
34	JUN	chr19:39970297-39972660	K562	blood:	n/a	n/a
35	POLR2A	chr19:39971123-39972091	GM19099	blood:	n/a	n/a
36	MAX	chr19:39971059-39972101	ECC-1	luminal epithelium:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
37	YY1	chr19:39971047-39972287	SK-N-SH	brain:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
38	REST	chr19:39970953-39972356	A549	lung:	n/a	chr19:39971694-39971708
39	USF1	chr19:39971026-39972108	A549	lung:	n/a	n/a
40	SP1	chr19:39970815-39972142	A549	lung:	n/a	chr19:39972077-39972086 chr19:39972078-39972087 chr19:39971799-39971813 chr19:39971825-39971839 chr19:39971766-39971780
41	POLR2A	chr19:39971132-39972079	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr19:39970150-39972565	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:39971132-39972103	HepG2	liver:	n/a	n/a
44	ZNF263	chr19:39971164-39972723	HEK293-T-REx	kidney:	n/a	chr19:39971827-39971836
45	POLR2A	chr19:39971082-39972116	GM12891	blood:	n/a	n/a
46	POLR2A	chr19:39971081-39972262	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:39971013-39972125	K562	blood:	n/a	n/a
48	FOSL2	chr19:39971054-39972083	A549	lung:	n/a	n/a
49	ETS1	chr19:39971064-39972129	A549	lung:	n/a	chr19:39971797-39971810 chr19:39971089-39971102
50	CREB1	chr19:39971035-39972208	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39934091..39937562-chr19:39970121..39972977,5	K562	blood:
2	chr19:39934091..39937114-chr19:39969895..39972879,3	K562	blood:
3	chr19:39969179..39972823-chr19:40019268..40024259,8	K562	blood:
4	chr19:39962317..39966816-chr19:39969995..39972771,6	MCF-7	breast:
5	chr19:39970388..39973416-chr19:39987093..39991960,6	MCF-7	breast:
6	chr19:39971121..39973511-chr19:39973741..39976891,3	MCF-7	breast:
7	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
8	chr19:39934676..39937838-chr19:39970025..39973557,7	MCF-7	breast:
9	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
10	chr19:39969762..39972823-chr19:40020818..40024781,5	K562	blood:
11	chr19:39962880..39966942-chr19:39968746..39972707,4	K562	blood:
12	chr19:39926650..39928509-chr19:39969774..39972138,2	MCF-7	breast:
13	chr19:39971313..39973393-chr19:39989065..39991077,2	MCF-7	breast:
14	chr19:39902436..39904048-chr19:39969524..39972192,2	K562	blood:
15	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:
16	chr19:39955020..39957486-chr19:39970318..39972255,2	MCF-7	breast:
17	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
18	chr19:39934619..39937838-chr19:39970480..39972998,6	MCF-7	breast:
19	chr19:39960496..39962184-chr19:39970692..39973089,3	MCF-7	breast:
20	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000176401	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10420073	0.84[ASN][1000 genomes]
rs10423921	0.84[ASN][1000 genomes]
rs10425652	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10426543	0.84[ASN][1000 genomes]
rs11882744	0.89[ASN][1000 genomes]
rs1529733	0.82[ASN][1000 genomes]
rs3786950	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45568533	0.84[ASN][1000 genomes]
rs4802030	0.84[ASN][1000 genomes]
rs4802032	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802033	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803244	0.84[ASN][1000 genomes]
rs4803248	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59269050	0.82[ASN][1000 genomes]
rs61480418	0.84[ASN][1000 genomes]
rs62120691	0.89[ASN][1000 genomes]
rs7245986	0.84[ASN][1000 genomes]
rs7246329	0.81[ASN][1000 genomes]
rs73035459	0.85[ASN][1000 genomes]
rs73035461	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
rs8106642	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	chr19:39970400-39972600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:39970600-39972400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr19:39970600-39972600	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr19:39970800-39972200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:39970800-39972200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39970800-39972200	Active TSS	Fetal Kidney	kidney
7	chr19:39970800-39972200	Active TSS	Psoas Muscle	Psoas
8	chr19:39970800-39972400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39970800-39972600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:39970800-39972600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:39970800-39972600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:39970800-39972600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:39971000-39972200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr19:39971000-39972200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:39971000-39972200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:39971000-39972200	Active TSS	Fetal Intestine Large	intestine
17	chr19:39971000-39972200	Active TSS	Gastric	stomach
18	chr19:39971000-39972200	Active TSS	Lung	lung
19	chr19:39971000-39972200	Active TSS	Ovary	ovary
20	chr19:39971000-39972200	Active TSS	NHDF-Ad	bronchial
21	chr19:39971000-39972400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:39971000-39972400	Active TSS	Aorta	Aorta
23	chr19:39971000-39972400	Active TSS	HSMM	muscle
24	chr19:39971000-39972600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr19:39971000-39973000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:39971200-39972200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr19:39971200-39972200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:39971200-39972200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:39971200-39972200	Active TSS	Colon Smooth Muscle	Colon
30	chr19:39971200-39972200	Active TSS	Fetal Heart	heart
31	chr19:39971200-39972200	Active TSS	Fetal Intestine Small	intestine
32	chr19:39971200-39972200	Active TSS	Small Intestine	intestine
33	chr19:39971200-39972200	Active TSS	GM12878-XiMat	blood
34	chr19:39971200-39972200	Active TSS	Hela-S3	cervix
35	chr19:39971200-39972200	Active TSS	HMEC	breast
36	chr19:39971200-39972200	Active TSS	HSMMtube	muscle
37	chr19:39971200-39972400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr19:39971200-39972400	Active TSS	A549	lung
39	chr19:39971200-39972600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:39971200-39972600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:39971200-39972600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:39971200-39972600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:39971200-39972600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:39971200-39973000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:39971400-39972200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:39971400-39972200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:39971400-39972200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:39971400-39972200	Active TSS	NH-A	brain
49	chr19:39971400-39972200	Active TSS	NHEK	skin
50	chr19:39971400-39972200	Active TSS	NHLF	lung

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