Variant report

Variant	rs4802088
Chromosome Location	chr19:41255768-41255769
allele	C/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	chr19:41255477-41257972	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:41255591-41257965	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:41255403-41257957	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:41255232-41256570	K562	blood:	n/a	n/a
5	PML	chr19:41255739-41255910	GM12878	blood:	n/a	n/a
6	BCL3	chr19:41255259-41258065	A549	lung:	n/a	n/a
7	PBX3	chr19:41255724-41257395	A549	lung:	n/a	chr19:41257023-41257032
8	MXI1	chr19:41255751-41257913	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:41255546-41257864	HCT-116	colon:	n/a	n/a
10	POLR2A	chr19:41255259-41257957	HL-60	blood:	n/a	n/a
11	POLR2A	chr19:41255355-41257801	NB4	blood:	n/a	n/a
12	POLR2A	chr19:41255732-41257397	HCT-116	colon:	n/a	n/a
13	TBL1XR1	chr19:41255729-41257824	K562	blood:	n/a	n/a
14	POLR2A	chr19:41255536-41257993	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:41255295-41258005	U87	brain:	n/a	n/a
16	POLR2A	chr19:41255276-41257951	GM12891	blood:	n/a	n/a
17	RCOR1	chr19:41255719-41256460	K562	blood:	n/a	n/a
18	ZBTB33	chr19:41255684-41257975	A549	lung:	n/a	chr19:41257090-41257105 chr19:41257098-41257107
19	BHLHE40	chr19:41255391-41257820	K562	blood:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256462-41256471
20	POLR2A	chr19:41255721-41258007	GM12878	blood:	n/a	n/a
21	MYC	chr19:41255359-41257881	K562	blood:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
22	POLR2A	chr19:41255731-41257877	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:41255251-41257877	K562	blood:	n/a	n/a
24	REST	chr19:41255601-41256557	A549	lung:	n/a	n/a
25	TAF1	chr19:41255732-41257980	A549	lung:	n/a	n/a
26	POLR2A	chr19:41255728-41255780	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:41255185-41257990	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41255227-41257860	K562	blood:	n/a	n/a
29	USF2	chr19:41255739-41255853	K562	blood:	n/a	n/a
30	ESRRA	chr19:41255212-41258832	GM12878	blood:	n/a	chr19:41255368-41255382 chr19:41256561-41256571 chr19:41256561-41256571 chr19:41256557-41256573
31	RFX5	chr19:41255464-41258017	SK-N-SH	brain:	n/a	chr19:41256665-41256680 chr19:41256671-41256679 chr19:41256571-41256580 chr19:41256704-41256713
32	POLR2A	chr19:41255160-41257529	MCF-7	breast:	n/a	n/a
33	SP1	chr19:41255694-41258003	A549	lung:	n/a	chr19:41256757-41256766 chr19:41256694-41256715 chr19:41256624-41256633 chr19:41257021-41257042 chr19:41256624-41256633 chr19:41256725-41256746 chr19:41256755-41256766 chr19:41256493-41256507 chr19:41256623-41256632 chr19:41256622-41256634 chr19:41256755-41256767 chr19:41256623-41256633 chr19:41256755-41256767
34	SIX5	chr19:41255261-41259082	A549	lung:	n/a	n/a
35	RELA	chr19:41255755-41257923	GM19099	blood:	n/a	n/a
36	RFX5	chr19:41255574-41257877	IMR90	lung:	n/a	chr19:41256665-41256680 chr19:41256671-41256679 chr19:41256571-41256580 chr19:41256704-41256713
37	HEY1	chr19:41255700-41256576	K562	blood:	n/a	n/a
38	MTA3	chr19:41255285-41256381	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:41255544-41256487	GM12891	blood:	n/a	n/a
40	EP300	chr19:41255684-41258029	A549	lung:	n/a	chr19:41257198-41257207 chr19:41255879-41255888 chr19:41256615-41256628
41	POLR2A	chr19:41255247-41257921	GM19193	blood:	n/a	n/a
42	POLR2A	chr19:41255749-41257940	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr19:41255328-41257887	K562	blood:	n/a	n/a
44	REST	chr19:41255367-41257977	A549	lung:	n/a	n/a
45	IRF1	chr19:41255347-41257884	K562	blood:	n/a	chr19:41256755-41256769 chr19:41256442-41256456 chr19:41256736-41256745
46	POLR2A	chr19:41255504-41257945	HepG2	liver:	n/a	n/a
47	ZC3H11A	chr19:41255567-41255917	K562	blood:	n/a	n/a
48	SP1	chr19:41255745-41257973	HCT-116	colon:	n/a	chr19:41256757-41256766 chr19:41256694-41256715 chr19:41256624-41256633 chr19:41257021-41257042 chr19:41256624-41256633 chr19:41256725-41256746 chr19:41256755-41256766 chr19:41256493-41256507 chr19:41256623-41256632 chr19:41256622-41256634 chr19:41256755-41256767 chr19:41256623-41256633 chr19:41256755-41256767
49	POLR2A	chr19:41255665-41257400	ECC-1	luminal epithelium:	n/a	n/a
50	MYC	chr19:41255607-41258077	A549	lung:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471

No.	Distal block	Cell Line	Cell type
1	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
2	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
3	chr19:41082129..41084725-chr19:41255576..41257148,2	K562	blood:
4	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
5	chr19:41254747..41256268-chr19:41303480..41305851,2	MCF-7	breast:
6	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
7	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
8	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
9	chr19:41206945..41208497-chr19:41254996..41257251,2	K562	blood:
10	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:
11	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
12	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
13	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
14	chr19:41255216..41257049-chr19:41286171..41288357,2	MCF-7	breast:
15	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
16	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
17	chr19:41254272..41257133-chr19:41310784..41312768,2	MCF-7	breast:
18	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
19	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
20	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
21	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
22	chr19:41191987..41193561-chr19:41255476..41257809,2	K562	blood:
23	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
24	chr19:41081293..41083629-chr19:41254991..41257076,2	K562	blood:
25	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:

Variant related genes	Relation type
C19orf54	TF binding region
SNRPA	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000268797	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs34406232	1.00[MEX][hapmap]
rs4803362	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803365	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs4803367	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs62621363	1.00[AMR][1000 genomes];0.89[EUR][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1793665	chr19:41249508-41258355	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
4	esv1803061	chr19:41249508-41258355	Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41246200-41256000	Weak transcription	Aorta	Aorta
2	chr19:41246400-41255800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:41247200-41255800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:41251600-41256000	Weak transcription	Ovary	ovary
5	chr19:41254000-41255800	Enhancers	Primary B cells from cord blood	blood
6	chr19:41254000-41255800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:41254000-41255800	Flanking Active TSS	Dnd41	blood
8	chr19:41254400-41255800	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:41254400-41255800	Enhancers	Fetal Muscle Leg	muscle
10	chr19:41254400-41255800	Enhancers	Right Ventricle	heart
11	chr19:41254400-41255800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:41254400-41256000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:41254400-41256000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr19:41254400-41256000	Enhancers	Spleen	Spleen
15	chr19:41254600-41255800	Enhancers	Fetal Lung	lung
16	chr19:41254600-41255800	Enhancers	Lung	lung
17	chr19:41254600-41259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:41255000-41255800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:41255200-41255800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:41255200-41255800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr19:41255200-41255800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:41255200-41255800	Enhancers	Fetal Brain Male	brain
23	chr19:41255200-41255800	Enhancers	Fetal Heart	heart
24	chr19:41255200-41255800	Flanking Active TSS	GM12878-XiMat	blood
25	chr19:41255200-41255800	Flanking Active TSS	HepG2	liver
26	chr19:41255200-41256000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr19:41255200-41256000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:41255200-41256000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:41255200-41256200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:41255200-41256200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:41255200-41256200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:41255200-41256200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:41255200-41256200	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr19:41255200-41256200	Flanking Active TSS	A549	lung
35	chr19:41255200-41256200	Flanking Active TSS	Hela-S3	cervix
36	chr19:41255200-41256200	Flanking Active TSS	K562	blood
37	chr19:41255200-41256400	Flanking Active TSS	HMEC	breast
38	chr19:41255200-41256400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr19:41255400-41255800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr19:41255400-41255800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:41255400-41255800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr19:41255400-41255800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:41255400-41255800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:41255400-41255800	Flanking Active TSS	Esophagus	oesophagus
45	chr19:41255400-41255800	Enhancers	Fetal Stomach	stomach
46	chr19:41255400-41255800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr19:41255400-41256000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:41255400-41256000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:41255400-41256000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:41255400-41256000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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