Variant report

Variant	rs62120525
Chromosome Location	chr19:39728626-39728627
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	MAX	chr19:39728488-39728733	K562	blood:	n/a	n/a
2	CTCF	chr19:39728520-39728670	Caco-2	colon:	n/a	n/a
3	ZNF143	chr19:39728479-39728802	GM12878	blood:	n/a	n/a
4	EBF1	chr19:39728418-39728780	GM12878	blood:	n/a	chr19:39728601-39728612 chr19:39728602-39728612
5	MAX	chr19:39728553-39728748	HepG2	liver:	n/a	n/a
6	TCF3	chr19:39728460-39728793	GM12878	blood:	n/a	chr19:39728580-39728593 chr19:39728595-39728608
7	ELF1	chr19:39728285-39728942	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:39728334-39728838	GM12892	blood:	n/a	n/a
9	USF1	chr19:39728405-39728891	ECC-1	luminal epithelium:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
10	TCF12	chr19:39728502-39728709	GM12878	blood:	n/a	chr19:39728595-39728605
11	EBF1	chr19:39728362-39728809	GM12878	blood:	n/a	chr19:39728601-39728612 chr19:39728602-39728612
12	ZBTB7A	chr19:39728439-39728806	K562	blood:	n/a	n/a
13	USF2	chr19:39728481-39728776	HepG2	liver:	n/a	chr19:39728593-39728609 chr19:39728579-39728595 chr19:39728621-39728632
14	POLR2A	chr19:39728567-39728794	HCT-116	colon:	n/a	n/a
15	EGR1	chr19:39728556-39728878	K562	blood:	n/a	chr19:39728749-39728764 chr19:39728575-39728585 chr19:39728750-39728763 chr19:39728750-39728763
16	MAX	chr19:39728452-39728776	Hela-S3	cervix:	n/a	chr19:39728753-39728763
17	POLR2A	chr19:39728491-39728769	GM12878	blood:	n/a	n/a
18	MYC	chr19:39728477-39728765	MCF-7	breast:	n/a	chr19:39728753-39728763
19	ELF1	chr19:39728081-39728806	K562	blood:	n/a	n/a
20	MAX	chr19:39728412-39728820	NB4	blood:	n/a	chr19:39728753-39728763 chr19:39728797-39728807
21	ELF1	chr19:39728408-39728855	GM12878	blood:	n/a	n/a
22	E2F6	chr19:39728444-39728755	K562	blood:	n/a	chr19:39728580-39728590
23	USF2	chr19:39728468-39728788	GM12878	blood:	n/a	chr19:39728593-39728609 chr19:39728579-39728595 chr19:39728621-39728632
24	USF1	chr19:39728403-39728745	ECC-1	luminal epithelium:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
25	EGR1	chr19:39728484-39728952	MCF-7	breast:	n/a	chr19:39728749-39728764 chr19:39728575-39728585 chr19:39728750-39728763 chr19:39728750-39728763 chr19:39728541-39728554
26	CTCF	chr19:39728600-39728750	GM12868	blood:	n/a	n/a
27	POLR2A	chr19:39728468-39728809	GM12878	blood:	n/a	n/a
28	NFE2	chr19:39728575-39728653	GM12878	blood:	n/a	chr19:39728624-39728633
29	USF2	chr19:39728502-39728782	Hela-S3	cervix:	n/a	chr19:39728593-39728609 chr19:39728579-39728595 chr19:39728621-39728632
30	MYC	chr19:39728605-39728671	MCF-7	breast:	n/a	n/a
31	SP1	chr19:39728501-39728803	GM12878	blood:	n/a	chr19:39728531-39728545 chr19:39728535-39728544 chr19:39728577-39728586 chr19:39728575-39728587 chr19:39728535-39728545 chr19:39728575-39728587 chr19:39728534-39728546 chr19:39728534-39728546
32	POLR2A	chr19:39728429-39728843	GM18505	blood:	n/a	n/a
33	NR2F2	chr19:39728419-39728967	MCF-7	breast:	n/a	n/a
34	RFX5	chr19:39728555-39728694	Hela-S3	cervix:	n/a	n/a
35	USF1	chr19:39728501-39728814	H1-hESC	embryonic stem cell:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
36	USF1	chr19:39728492-39728763	GM12878	blood:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
37	MAZ	chr19:39728538-39728662	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:39728579-39728724	K562	blood:	n/a	n/a
39	MAX	chr19:39728362-39728899	ECC-1	luminal epithelium:	n/a	chr19:39728753-39728763 chr19:39728844-39728854 chr19:39728797-39728807
40	USF1	chr19:39728428-39728739	K562	blood:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
41	CHD2	chr19:39728561-39728708	Hela-S3	cervix:	n/a	n/a
42	STAT1	chr19:39728555-39728683	GM12878	blood:	n/a	chr19:39728665-39728672 chr19:39728610-39728621
43	MAX	chr19:39728363-39728853	HepG2	liver:	n/a	chr19:39728753-39728763 chr19:39728797-39728807
44	BHLHE40	chr19:39728457-39728802	HepG2	liver:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
45	ELF1	chr19:39728408-39728883	MCF-7	breast:	n/a	n/a
46	POLR2A	chr19:39728469-39728861	GM15510	blood:	n/a	n/a
47	USF1	chr19:39728531-39728735	SK-N-SH_RA	brain:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
48	PRDM1	chr19:39728409-39728820	Hela-S3	cervix:	n/a	chr19:39728608-39728623 chr19:39728609-39728622 chr19:39728613-39728622 chr19:39728609-39728623
49	MAX	chr19:39728495-39728703	GM12878	blood:	n/a	n/a
50	USF1	chr19:39728493-39728713	HepG2	liver:	n/a	chr19:39728593-39728609 chr19:39728579-39728595

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39727742..39730631-chr19:39743095..39745930,2	K562	blood:
2	chr19:39727142..39728696-chr19:39832975..39834941,2	K562	blood:

Variant related genes	Relation type
IFNL3P1	TF binding region
ENSG00000179134	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000213926	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11669865	1.00[AFR][1000 genomes]
rs45591338	1.00[AFR][1000 genomes]
rs45613331	1.00[AFR][1000 genomes]
rs62119541	1.00[AFR][1000 genomes]
rs62119730	1.00[AFR][1000 genomes]
rs62120527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62120528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62120532	1.00[AFR][1000 genomes]
rs62120669	1.00[AFR][1000 genomes]
rs62120671	1.00[AFR][1000 genomes]
rs62122884	1.00[AMR][1000 genomes]
rs73555604	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv518540	chr19:39697974-39731783	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv911678	chr19:39710903-39763765	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1796501	chr19:39723520-39740868	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv3377837	chr19:39727555-39735103	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv3510603	chr19:39727606-39735042	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv3510604	chr19:39727606-39735042	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39726600-39729400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:39726800-39729200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr19:39727200-39729000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:39727200-39729200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39727200-39729800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:39728000-39728800	Enhancers	Spleen	Spleen
7	chr19:39728000-39729000	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:39728000-39729000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr19:39728000-39729200	Enhancers	Primary B cells from peripheral blood	blood
10	chr19:39728000-39729200	Enhancers	Placenta	Placenta
11	chr19:39728200-39728800	Enhancers	Primary T cells from cord blood	blood
12	chr19:39728200-39728800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr19:39728200-39728800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:39728200-39728800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:39728200-39728800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:39728200-39728800	Enhancers	Liver	Liver
17	chr19:39728200-39728800	Enhancers	Esophagus	oesophagus
18	chr19:39728200-39728800	Active TSS	A549	lung
19	chr19:39728200-39729000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:39728200-39729000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:39728200-39729000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39728200-39729000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:39728200-39729000	Enhancers	Dnd41	blood
24	chr19:39728200-39729200	Enhancers	Stomach Mucosa	stomach
25	chr19:39728200-39729400	Enhancers	Primary B cells from cord blood	blood
26	chr19:39728400-39728800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr19:39728400-39728800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:39728400-39728800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:39728400-39728800	Flanking Active TSS	HepG2	liver
30	chr19:39728400-39729000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:39728400-39729000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:39728400-39729000	Enhancers	Duodenum Mucosa	Duodenum
33	chr19:39728400-39729000	Bivalent Enhancer	Fetal Intestine Large	intestine
34	chr19:39728400-39729000	Enhancers	Fetal Thymus	thymus
35	chr19:39728400-39729200	Enhancers	Thymus	Thymus
36	chr19:39728600-39728800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:39728600-39728800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39728600-39728800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
39	chr19:39728600-39728800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:39728600-39728800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr19:39728600-39728800	Flanking Active TSS	Pancreas	Pancrea
42	chr19:39728600-39728800	Flanking Active TSS	Hela-S3	cervix
43	chr19:39728600-39729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr19:39728600-39729000	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr19:39728600-39729000	Enhancers	GM12878-XiMat	blood
46	chr19:39728600-39729400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr19:39728600-39729600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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