Variant report

Variant	rs2607416
Chromosome Location	chr19:41260831-41260832
allele	A/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	STAT1	chr19:41260774-41261006	GM12878	blood:	n/a	n/a
2	PML	chr19:41260442-41261243	GM12878	blood:	n/a	n/a
3	HNF4G	chr19:41260339-41260833	HepG2	liver:	n/a	chr19:41260646-41260659 chr19:41260647-41260660 chr19:41260645-41260660 chr19:41260646-41260654 chr19:41260646-41260661 chr19:41260646-41260660 chr19:41260647-41260660 chr19:41260647-41260659 chr19:41260645-41260660 chr19:41260647-41260659 chr19:41260645-41260660 chr19:41260644-41260662 chr19:41260647-41260660 chr19:41260647-41260659 chr19:41260647-41260659 chr19:41260645-41260660
4	EBF1	chr19:41260637-41260966	GM12878	blood:	n/a	n/a
5	TCF12	chr19:41260264-41261289	A549	lung:	n/a	n/a
6	EP300	chr19:41260807-41261074	GM12878	blood:	n/a	n/a
7	RUNX3	chr19:41260553-41261203	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:41260016-41261081	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBL1XR1	chr19:41260774-41261068	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:41259776-41262416	HepG2	liver:	n/a	n/a
11	CHD2	chr19:41260544-41261076	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:41260348-41260927	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:41260143-41261081	GM12878	blood:	n/a	n/a
14	MAZ	chr19:41260606-41260910	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:41260214-41261089	GM12892	blood:	n/a	n/a
16	EP300	chr19:41260472-41261028	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:41260610-41261010	GM12878	blood:	n/a	n/a
18	CUX1	chr19:41260670-41260977	GM12878	blood:	n/a	n/a
19	RCOR1	chr19:41260615-41260982	GM12878	blood:	n/a	n/a
20	FOSL2	chr19:41260285-41260922	A549	lung:	n/a	n/a
21	RAD21	chr19:41260638-41260896	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:41260087-41261142	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr19:41260132-41260997	SK-N-MC	brain:	n/a	n/a
24	CTCF	chr19:41260720-41260870	HepG2	liver:	n/a	chr19:41260855-41260864
25	TFAP2C	chr19:41260421-41260872	Hela-S3	cervix:	n/a	chr19:41260653-41260668
26	SMC3	chr19:41260820-41261019	GM12878	blood:	n/a	chr19:41260854-41260862
27	POU2F2	chr19:41260539-41261196	GM12878	blood:	n/a	n/a
28	CHD1	chr19:41260440-41261022	GM12878	blood:	n/a	n/a
29	NFIC	chr19:41260580-41261245	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:41260232-41261101	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:41259522-41260877	K562	blood:	n/a	n/a
32	SIN3A	chr19:41260716-41261064	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:41260490-41260860	HL-60	blood:	n/a	n/a
34	REST	chr19:41260310-41261060	A549	lung:	n/a	chr19:41260900-41260913 chr19:41260687-41260700
35	POLR2A	chr19:41260288-41260974	HepG2	liver:	n/a	n/a
36	RUNX3	chr19:41260386-41261068	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:41260551-41260864	H1-hESC	embryonic stem cell:	n/a	n/a
38	STAT5A	chr19:41260377-41261019	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:41260017-41261010	GM12892	blood:	n/a	n/a
40	IKZF1	chr19:41260613-41261001	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:41260204-41260859	K562	blood:	n/a	n/a
42	POLR2A	chr19:41260361-41261060	GM12878	blood:	n/a	n/a
43	CEBPB	chr19:41260699-41261204	A549	lung:	n/a	chr19:41261037-41261048 chr19:41260875-41260888
44	IRF4	chr19:41260670-41261135	GM12878	blood:	n/a	n/a
45	TFAP2A	chr19:41260421-41260867	Hela-S3	cervix:	n/a	chr19:41260654-41260665 chr19:41260653-41260668
46	WRNIP1	chr19:41260371-41261135	GM12878	blood:	n/a	n/a
47	MTA3	chr19:41260198-41261185	GM12878	blood:	n/a	n/a
48	BHLHE40	chr19:41260647-41261382	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:41260319-41260887	K562	blood:	n/a	n/a
50	BCLAF1	chr19:41260665-41261223	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41260700..41263624-chr19:41281746..41284711,4	K562	blood:
2	chr19:41260139..41263549-chr19:41263654..41270764,10	MCF-7	breast:
3	chr19:41222403..41224199-chr19:41258986..41261633,2	MCF-7	breast:
4	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
5	chr19:41206422..41208384-chr19:41260383..41263313,2	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10420651	0.84[CHB][hapmap]
rs10420685	0.84[CHB][hapmap]
rs13108	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1455434	0.92[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs17726258	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1869710	0.92[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2230694	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233153	0.95[ASN][1000 genomes]
rs2233154	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2233156	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2233159	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249854	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254326	0.84[CHB][hapmap]
rs2279699	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2303723	0.84[CHB][hapmap]
rs2545777	0.84[ASN][1000 genomes]
rs2545778	0.84[ASN][1000 genomes]
rs2561531	0.92[CHB][hapmap]
rs2604876	0.85[ASN][1000 genomes]
rs2604877	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2604910	0.92[JPT][hapmap]
rs2607411	0.87[ASN][1000 genomes]
rs2607412	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2607413	0.87[ASN][1000 genomes]
rs2607418	0.84[CHB][hapmap]
rs2607419	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607421	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607422	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607423	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607425	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607426	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644917	0.82[ASN][1000 genomes]
rs56891752	0.84[ASN][1000 genomes]
rs60533951	0.80[ASN][1000 genomes]
rs8107978	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109099	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
4	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
5	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2607416	C19orf54	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41261200	Weak transcription	Aorta	Aorta
2	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:41258400-41261400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:41258400-41261600	Weak transcription	HSMMtube	muscle
5	chr19:41258400-41265200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:41258600-41262400	Genic enhancers	Fetal Thymus	thymus
7	chr19:41258800-41268400	Weak transcription	Psoas Muscle	Psoas
8	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:41259200-41264200	Weak transcription	Fetal Brain Male	brain
10	chr19:41259200-41272800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr19:41259600-41262600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:41259800-41261000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
13	chr19:41259800-41261200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr19:41259800-41261600	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr19:41259800-41261800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:41259800-41261800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr19:41259800-41262200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr19:41259800-41263200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:41260000-41261000	Flanking Active TSS	Fetal Intestine Large	intestine
20	chr19:41260000-41261200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr19:41260000-41261200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:41260000-41261600	Enhancers	Ovary	ovary
23	chr19:41260000-41262000	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr19:41260000-41263000	Genic enhancers	Lung	lung
25	chr19:41260000-41263000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
26	chr19:41260000-41263200	Genic enhancers	Fetal Muscle Leg	muscle
27	chr19:41260200-41261000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
28	chr19:41260200-41261000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
29	chr19:41260200-41261000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:41260200-41261000	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr19:41260200-41261000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:41260200-41261000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:41260200-41261000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:41260200-41261000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr19:41260200-41261000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr19:41260200-41261000	Transcr. at gene 5' and 3'	A549	lung
37	chr19:41260200-41261000	Transcr. at gene 5' and 3'	K562	blood
38	chr19:41260200-41261000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr19:41260200-41261000	Transcr. at gene 5' and 3'	NH-A	brain
40	chr19:41260200-41261200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:41260200-41261200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
42	chr19:41260200-41261200	Genic enhancers	Left Ventricle	heart
43	chr19:41260200-41261400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:41260200-41261600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:41260200-41261600	Genic enhancers	Brain Angular Gyrus	brain
46	chr19:41260200-41261800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:41260200-41261800	Genic enhancers	Fetal Stomach	stomach
48	chr19:41260200-41261800	Enhancers	Right Atrium	heart
49	chr19:41260200-41261800	Genic enhancers	NHEK	skin
50	chr19:41260200-41262000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links