Variant report

Variant	rs2254343
Chromosome Location	chr19:41255500-41255501
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	chr19:41255477-41257972	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:41255403-41257957	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:41255165-41255722	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:41255232-41256570	K562	blood:	n/a	n/a
5	BCL3	chr19:41255259-41258065	A549	lung:	n/a	n/a
6	POLR2A	chr19:41255404-41255620	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41255259-41257957	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:41255355-41257801	NB4	blood:	n/a	n/a
9	POLR2A	chr19:41255295-41258005	U87	brain:	n/a	n/a
10	UBTF	chr19:41255327-41255609	K562	blood:	n/a	n/a
11	POLR2A	chr19:41255276-41257951	GM12891	blood:	n/a	n/a
12	BHLHE40	chr19:41255391-41257820	K562	blood:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256462-41256471
13	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
14	POLR2A	chr19:41255251-41257877	K562	blood:	n/a	n/a
15	RCOR1	chr19:41255287-41255645	K562	blood:	n/a	n/a
16	POLR2A	chr19:41255185-41257990	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:41255227-41257860	K562	blood:	n/a	n/a
18	ESRRA	chr19:41255212-41258832	GM12878	blood:	n/a	chr19:41255368-41255382 chr19:41256561-41256571 chr19:41256561-41256571 chr19:41256557-41256573
19	RFX5	chr19:41255464-41258017	SK-N-SH	brain:	n/a	chr19:41256665-41256680 chr19:41256671-41256679 chr19:41256571-41256580 chr19:41256704-41256713
20	POLR2A	chr19:41255160-41257529	MCF-7	breast:	n/a	n/a
21	SIX5	chr19:41255261-41259082	A549	lung:	n/a	n/a
22	TEAD4	chr19:41255287-41255702	K562	blood:	n/a	n/a
23	MTA3	chr19:41255285-41256381	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:41255247-41257921	GM19193	blood:	n/a	n/a
25	ZBTB7A	chr19:41255156-41255767	K562	blood:	n/a	n/a
26	EP300	chr19:41255380-41255615	K562	blood:	n/a	n/a
27	POLR2A	chr19:41255328-41257887	K562	blood:	n/a	n/a
28	REST	chr19:41255367-41257977	A549	lung:	n/a	n/a
29	IRF1	chr19:41255347-41257884	K562	blood:	n/a	chr19:41256755-41256769 chr19:41256442-41256456 chr19:41256736-41256745
30	POLR2A	chr19:41255155-41258062	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:41255130-41259372	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:41255201-41258657	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr19:41255372-41257982	GM12891	blood:	n/a	n/a
34	ZBTB7A	chr19:41255218-41255661	K562	blood:	n/a	n/a
35	POLR2A	chr19:41255371-41257841	Raji	blood:	n/a	n/a
36	YY1	chr19:41255356-41255564	K562	blood:	n/a	n/a
37	GATA1	chr19:41255198-41255810	PBDE	blood:	n/a	chr19:41255740-41255751
38	POLR2A	chr19:41255253-41258081	GM12892	blood:	n/a	n/a
39	E2F6	chr19:41255326-41257802	K562	blood:	n/a	chr19:41256760-41256770 chr19:41256736-41256745 chr19:41256721-41256736 chr19:41256805-41256815 chr19:41256721-41256736 chr19:41256442-41256453
40	POLR2A	chr19:41255463-41257911	GM18951	blood:	n/a	n/a
41	UBTF	chr19:41255248-41255714	K562	blood:	n/a	n/a
42	MAX	chr19:41255316-41255637	K562	blood:	n/a	n/a
43	POLR2A	chr19:41255119-41257953	K562	blood:	n/a	n/a
44	POLR2A	chr19:41255463-41257952	GM18505	blood:	n/a	n/a
45	POLR2A	chr19:41255333-41257763	MCF-7	breast:	n/a	n/a
46	E2F6	chr19:41255372-41255513	K562	blood:	n/a	n/a
47	MAX	chr19:41255345-41255601	K562	blood:	n/a	n/a
48	POLR2A	chr19:41255484-41257827	GM18526	blood:	n/a	n/a
49	ZMIZ1	chr19:41255342-41257729	K562	blood:	n/a	n/a
50	NR2F2	chr19:41255321-41256625	K562	blood:	n/a	n/a

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	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
4	chr19:41254747..41256268-chr19:41303480..41305851,2	MCF-7	breast:
5	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
6	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
7	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
8	chr19:41206945..41208497-chr19:41254996..41257251,2	K562	blood:
9	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:
10	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
11	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
12	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
13	chr19:41255216..41257049-chr19:41286171..41288357,2	MCF-7	breast:
14	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
15	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
16	chr19:41254272..41257133-chr19:41310784..41312768,2	MCF-7	breast:
17	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
18	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
19	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
20	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
21	chr19:41191987..41193561-chr19:41255476..41257809,2	K562	blood:
22	chr19:41253175..41255589-chr19:41255801..41257660,2	MCF-7	breast:
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
SNRPA	TF binding region
C19orf54	TF binding region
ENSG00000105323	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000268797	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1457141	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2369302	0.84[CEU][hapmap]
rs2604874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607420	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7254893	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2254343	C19orf54	Cis_1M	lymphoblastoid	RTeQTL
rs2254343	C19orf54	cis	Thyroid	GTEx
rs2254343	C19orf54	cis	Lymphoblastoid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41240200-41255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:41242200-41255600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:41243600-41255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:41245600-41255600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:41246000-41255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr19:41246200-41255600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:41246200-41255600	Weak transcription	Small Intestine	intestine
8	chr19:41246200-41256000	Weak transcription	Aorta	Aorta
9	chr19:41246400-41255800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:41246800-41255600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:41247200-41255800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:41248400-41255600	Weak transcription	Primary T cells from cord blood	blood
13	chr19:41250400-41255600	Weak transcription	Gastric	stomach
14	chr19:41251600-41255600	Weak transcription	Fetal Kidney	kidney
15	chr19:41251600-41255600	Weak transcription	HUVEC	blood vessel
16	chr19:41251600-41255600	Weak transcription	NH-A	brain
17	chr19:41251600-41256000	Weak transcription	Ovary	ovary
18	chr19:41252000-41255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:41252200-41255600	Weak transcription	Osteobl	bone
20	chr19:41253600-41255600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr19:41253800-41255600	Enhancers	Placenta	Placenta
22	chr19:41254000-41255600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr19:41254000-41255600	Enhancers	Fetal Muscle Trunk	muscle
24	chr19:41254000-41255800	Enhancers	Primary B cells from cord blood	blood
25	chr19:41254000-41255800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:41254000-41255800	Flanking Active TSS	Dnd41	blood
27	chr19:41254200-41255600	Enhancers	Adipose Nuclei	Adipose
28	chr19:41254200-41255600	Enhancers	Fetal Thymus	thymus
29	chr19:41254400-41255600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:41254400-41255600	Enhancers	Left Ventricle	heart
31	chr19:41254400-41255600	Enhancers	NHLF	lung
32	chr19:41254400-41255800	Enhancers	Primary B cells from peripheral blood	blood
33	chr19:41254400-41255800	Enhancers	Fetal Muscle Leg	muscle
34	chr19:41254400-41255800	Enhancers	Right Ventricle	heart
35	chr19:41254400-41255800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr19:41254400-41256000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:41254400-41256000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr19:41254400-41256000	Enhancers	Spleen	Spleen
39	chr19:41254600-41255600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:41254600-41255600	Enhancers	Brain Anterior Caudate	brain
41	chr19:41254600-41255600	Enhancers	Brain Hippocampus Middle	brain
42	chr19:41254600-41255600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr19:41254600-41255600	Enhancers	Right Atrium	heart
44	chr19:41254600-41255800	Enhancers	Fetal Lung	lung
45	chr19:41254600-41255800	Enhancers	Lung	lung
46	chr19:41254600-41259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:41255000-41255600	Enhancers	Colonic Mucosa	Colon
48	chr19:41255000-41255800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:41255200-41255600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr19:41255200-41255600	Enhancers	Muscle Satellite Cultured Cells	--

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