Variant report

Variant	rs2304221
Chromosome Location	chr19:39971622-39971623
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	chr19:39971072-39972241	H1-hESC	embryonic stem cell:	n/a	n/a
2	HCFC1	chr19:39970889-39972362	Hela-S3	cervix:	n/a	n/a
3	TAL1	chr19:39971130-39971658	K562	blood:	n/a	n/a
4	PBX3	chr19:39970940-39971859	A549	lung:	n/a	n/a
5	HEY1	chr19:39970975-39971799	K562	blood:	n/a	n/a
6	POLR2A	chr19:39971103-39971926	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:39970896-39972437	GM12891	blood:	n/a	n/a
8	TEAD4	chr19:39970981-39971661	K562	blood:	n/a	n/a
9	YY1	chr19:39971125-39972129	ECC-1	luminal epithelium:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
10	ETS1	chr19:39971002-39972169	A549	lung:	n/a	chr19:39971797-39971810 chr19:39972147-39972156 chr19:39971089-39971102
11	POLR2A	chr19:39971095-39972002	GM18505	blood:	n/a	n/a
12	TAF1	chr19:39971074-39971813	HepG2	liver:	n/a	n/a
13	HMGN3	chr19:39971173-39971695	K562	blood:	n/a	n/a
14	POLR2A	chr19:39971073-39971755	HCT-116	colon:	n/a	n/a
15	CREB1	chr19:39971060-39971870	HepG2	liver:	n/a	n/a
16	MYC	chr19:39971225-39971969	MCF-7	breast:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
17	MAZ	chr19:39970989-39971713	K562	blood:	n/a	n/a
18	YY1	chr19:39971047-39972012	HepG2	liver:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
19	HEY1	chr19:39971148-39971975	HepG2	liver:	n/a	n/a
20	USF1	chr19:39971071-39972077	ECC-1	luminal epithelium:	n/a	n/a
21	CHD2	chr19:39971173-39971870	HepG2	liver:	n/a	n/a
22	ELF1	chr19:39971029-39971791	GM12878	blood:	n/a	n/a
23	REST	chr19:39971013-39971877	HL-60	blood:	n/a	chr19:39971694-39971708
24	YY1	chr19:39971053-39972178	GM12878	blood:	n/a	chr19:39971485-39971502 chr19:39971985-39971995 chr19:39971985-39972007
25	MAX	chr19:39971207-39971968	HepG2	liver:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
26	UBTF	chr19:39971165-39971679	K562	blood:	n/a	n/a
27	POLR2A	chr19:39971067-39971659	HepG2	liver:	n/a	n/a
28	CHD1	chr19:39971163-39972137	GM12878	blood:	n/a	n/a
29	FOSL2	chr19:39970895-39972340	A549	lung:	n/a	n/a
30	POLR2A	chr19:39970952-39972248	GM12892	blood:	n/a	n/a
31	MAX	chr19:39971065-39972002	NB4	blood:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
32	ATF3	chr19:39971213-39971800	K562	blood:	n/a	n/a
33	BCL3	chr19:39971248-39971748	GM12878	blood:	n/a	n/a
34	YY1	chr19:39971176-39971899	GM12891	blood:	n/a	chr19:39971485-39971502
35	MXI1	chr19:39970630-39972480	SK-N-SH	brain:	n/a	chr19:39971811-39971820 chr19:39971813-39971822
36	YY1	chr19:39971239-39971913	HCT-116	colon:	n/a	chr19:39971485-39971502
37	POLR2A	chr19:39971056-39972009	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr19:39971232-39971826	A549	lung:	n/a	n/a
39	POLR2A	chr19:39971103-39971818	NB4	blood:	n/a	n/a
40	SIN3AK20	chr19:39970991-39972108	A549	lung:	n/a	n/a
41	POLR2A	chr19:39971099-39971767	HepG2	liver:	n/a	n/a
42	MAX	chr19:39970953-39972144	HepG2	liver:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
43	MYC	chr19:39970996-39971995	MCF10A-Er-Src	breast:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
44	BCL3	chr19:39970721-39971934	A549	lung:	n/a	n/a
45	TAF1	chr19:39971308-39971632	GM12892	blood:	n/a	n/a
46	E2F6	chr19:39971084-39971749	K562	blood:	n/a	chr19:39971726-39971737
47	MYBL2	chr19:39971044-39971680	HepG2	liver:	n/a	n/a
48	TCF12	chr19:39971105-39971973	ECC-1	luminal epithelium:	n/a	chr19:39971783-39971790
49	MYC	chr19:39970950-39971859	K562	blood:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
50	POLR2A	chr19:39971129-39971923	Gliobla	brain:	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	chr19:39969776..39971710-chr8:125561754..125564240,2	MCF-7	breast:
15	chr19:39902436..39904048-chr19:39969524..39972192,2	K562	blood:
16	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:
17	chr19:39955020..39957486-chr19:39970318..39972255,2	MCF-7	breast:
18	chr19:39971112..39971648-chr22:19165745..19166658,2	HCT-116	colon:
19	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
20	chr19:39970882..39971709-chr7:104653342..104654017,2	Hela-S3	cervix:
21	chr19:39934619..39937838-chr19:39970480..39972998,6	MCF-7	breast:
22	chr19:39960496..39962184-chr19:39970692..39973089,3	MCF-7	breast:
23	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000090932	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000100075	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10412931	0.90[EUR][1000 genomes]
rs10423537	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10424217	0.89[EUR][1000 genomes]
rs1110627	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1130180	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609112	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12978920	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12978954	0.84[EUR][1000 genomes]
rs12979605	0.83[EUR][1000 genomes]
rs12983040	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1529732	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560730	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1865091	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865092	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1932	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009970	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060270	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060271	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060272	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2116932	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288933	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288934	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304219	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353678	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353679	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs251855	0.89[EUR][1000 genomes]
rs251856	0.88[EUR][1000 genomes]
rs251857	0.89[EUR][1000 genomes]
rs251858	0.89[EUR][1000 genomes]
rs251859	0.88[EUR][1000 genomes]
rs251860	0.85[EUR][1000 genomes]
rs28528765	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28620146	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28637729	0.87[EUR][1000 genomes]
rs28649498	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31727	0.80[EUR][1000 genomes]
rs34918990	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35647910	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4390710	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802026	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802031	0.81[AMR][1000 genomes]
rs4803237	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803240	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803241	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803242	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803245	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803246	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803247	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803250	0.88[EUR][1000 genomes]
rs566130	0.89[EUR][1000 genomes]
rs59007555	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508862	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6508863	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508864	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508865	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686956	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7251384	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251652	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255253	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73035416	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73549933	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107194	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107647	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110134	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110716	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111260	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878754	0.96[EUR][1000 genomes];0.90[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
rs2304221	RPS16	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39970400-39972000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:39970400-39972600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:39970600-39972000	Active TSS	Brain Germinal Matrix	brain
4	chr19:39970600-39972000	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:39970600-39972400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:39970600-39972600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr19:39970800-39972000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:39970800-39972000	Active TSS	Brain Substantia Nigra	brain
9	chr19:39970800-39972000	Active TSS	Osteobl	bone
10	chr19:39970800-39972200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:39970800-39972200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39970800-39972200	Active TSS	Fetal Kidney	kidney
13	chr19:39970800-39972200	Active TSS	Psoas Muscle	Psoas
14	chr19:39970800-39972400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:39970800-39972600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr19:39970800-39972600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr19:39970800-39972600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr19:39970800-39972600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr19:39971000-39971800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr19:39971000-39971800	Active TSS	Spleen	Spleen
21	chr19:39971000-39972000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:39971000-39972000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr19:39971000-39972000	Active TSS	Brain Angular Gyrus	brain
24	chr19:39971000-39972000	Active TSS	Brain Cingulate Gyrus	brain
25	chr19:39971000-39972000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:39971000-39972000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr19:39971000-39972000	Active TSS	Esophagus	oesophagus
28	chr19:39971000-39972000	Active TSS	Fetal Brain Female	brain
29	chr19:39971000-39972000	Active TSS	Fetal Stomach	stomach
30	chr19:39971000-39972000	Active TSS	Left Ventricle	heart
31	chr19:39971000-39972000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr19:39971000-39972000	Active TSS	Right Ventricle	heart
33	chr19:39971000-39972200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr19:39971000-39972200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:39971000-39972200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:39971000-39972200	Active TSS	Fetal Intestine Large	intestine
37	chr19:39971000-39972200	Active TSS	Gastric	stomach
38	chr19:39971000-39972200	Active TSS	Lung	lung
39	chr19:39971000-39972200	Active TSS	Ovary	ovary
40	chr19:39971000-39972200	Active TSS	NHDF-Ad	bronchial
41	chr19:39971000-39972400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:39971000-39972400	Active TSS	Aorta	Aorta
43	chr19:39971000-39972400	Active TSS	HSMM	muscle
44	chr19:39971000-39972600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr19:39971000-39973000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:39971200-39971800	Active TSS	Primary T cells from cord blood	blood
47	chr19:39971200-39971800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
48	chr19:39971200-39971800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:39971200-39971800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:39971200-39971800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links