Variant report

Variant	rs2073899
Chromosome Location	chr19:35752917-35752918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:35752507-35753333	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:35752888-35753704	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:35752892-35753836	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:35752562-35753576	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:35752231-35753813	ECC-1	luminal epithelium:	n/a	n/a
6	BCL3	chr19:35752530-35753795	A549	lung:	n/a	n/a
7	POLR2A	chr19:35751416-35753773	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:35751992-35753868	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:35751612-35760840	K562	blood:	n/a	n/a
10	POLR2A	chr19:35752437-35753883	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:35752466-35753059	U87	brain:	n/a	n/a
12	POLR2A	chr19:35751524-35759415	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:35752856-35753600	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:35752369-35753946	HEK293	kidney:	n/a	n/a
15	POLR2A	chr19:35751840-35753818	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr19:35752444-35752926	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:35752883-35753178	K562	blood:	n/a	n/a
18	POLR2A	chr19:35752907-35754050	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr19:35752800-35753531	U87	brain:	n/a	n/a
20	POLR2A	chr19:35752220-35753759	A549	lung:	n/a	n/a
21	POLR2A	chr19:35752316-35753688	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr19:35751581-35753714	A549	lung:	n/a	n/a
23	POLR2A	chr19:35752817-35753219	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:35752306-35753732	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:35751638-35753929	HepG2	liver:	n/a	n/a
26	POLR2A	chr19:35752868-35753443	HCT-116	colon:	n/a	n/a
27	POLR2A	chr19:35751616-35753771	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:35751530-35754083	Hela-S3	cervix:	n/a	n/a
29	PBX3	chr19:35751739-35753829	A549	lung:	n/a	n/a
30	POLR2A	chr19:35752800-35753542	U87	brain:	n/a	n/a
31	POLR2A	chr19:35752075-35759311	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:35751722-35753917	K562	blood:	n/a	n/a
33	POLR2A	chr19:35751472-35759661	MCF10A-Er-Src	breast:	n/a	n/a
34	PBX3	chr19:35752778-35753737	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr19:35752884-35753623	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:35752883-35753029	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:35751566-35753945	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr19:35752409-35753692	GM19193	blood:	n/a	n/a
39	BCL3	chr19:35751811-35753987	A549	lung:	n/a	n/a
40	PBX3	chr19:35752635-35753646	A549	lung:	n/a	n/a
41	POLR2A	chr19:35752832-35753796	HepG2	liver:	n/a	n/a
42	POLR2A	chr19:35751461-35753851	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:35752263-35753823	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr19:35752809-35753849	HL-60	blood:	n/a	n/a
45	POLR2A	chr19:35752518-35753713	GM15510	blood:	n/a	n/a
46	POLR2A	chr19:35752222-35753820	K562	blood:	n/a	n/a
47	ELF1	chr19:35752742-35753681	A549	lung:	n/a	chr19:35753417-35753429
48	POLR2A	chr19:35752868-35753133	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:35751582-35753781	GM18505	blood:	n/a	n/a
50	POLR2A	chr19:35751706-35753919	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35657563..35659340-chr19:35750773..35753172,2	K562	blood:
2	chr19:35752101..35756218-chr19:36205472..36209304,3	MCF-7	breast:
3	chr19:35644270..35647096-chr19:35751506..35754476,2	K562	blood:
4	chr19:35632127..35634031-chr19:35752023..35753899,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268947	TF binding region
LSR	TF binding region
ENSG00000153902	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000089327	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10405246	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410675	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414846	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419261	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419959	0.87[ASW][hapmap];0.85[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10421096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421504	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421599	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421768	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424619	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051995	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052033	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973672	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974791	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975284	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979058	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979792	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981527	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984022	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985618	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986033	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345192	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280744	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280745	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280747	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365133	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365136	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832786	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250673	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497966	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35959789	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564117	0.83[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs62109572	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112772	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71352913	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256866	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101606	0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
10	nsv911620	chr19:35752917-35771382	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
11	nsv911621	chr19:35752917-35772471	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
12	nsv911622	chr19:35752917-35773146	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
13	nsv911623	chr19:35752917-35775441	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2073899	ZFP36	cis	parietal	SCAN
rs2073899	HNRNPUL1	cis	cerebellum	SCAN
rs2073899	SERTAD3	cis	cerebellum	SCAN
rs2073899	U2AF1L4	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35741200-35758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:35741400-35757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:35742000-35756200	Strong transcription	NHEK	skin
4	chr19:35742600-35755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:35743800-35756600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr19:35744400-35757600	Strong transcription	Fetal Intestine Large	intestine
7	chr19:35744800-35757600	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr19:35744800-35757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:35744800-35757800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr19:35744800-35758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:35745000-35757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:35746200-35755200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:35746600-35755000	Weak transcription	GM12878-XiMat	blood
14	chr19:35746600-35757600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:35746600-35757600	Weak transcription	Hela-S3	cervix
16	chr19:35746800-35756000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:35747600-35755200	Weak transcription	Fetal Heart	heart
18	chr19:35747800-35755400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:35747800-35755600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:35748400-35756000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr19:35748800-35756600	Weak transcription	Primary T cells from cord blood	blood
22	chr19:35748800-35757600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:35749000-35753000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:35749000-35753800	Strong transcription	Esophagus	oesophagus
25	chr19:35749000-35755000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:35749000-35756000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:35749000-35756200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:35749000-35756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:35749000-35757000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:35749000-35758000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:35749200-35753800	Strong transcription	HepG2	liver
32	chr19:35749200-35754000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:35749200-35756200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:35749200-35756600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:35749400-35757600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr19:35749600-35755000	Weak transcription	Fetal Kidney	kidney
37	chr19:35749800-35754000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:35749800-35755200	Weak transcription	Spleen	Spleen
39	chr19:35750200-35755000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:35750200-35755200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:35750400-35753800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:35750600-35754000	Strong transcription	HMEC	breast
43	chr19:35750600-35754000	Strong transcription	K562	blood
44	chr19:35750600-35755600	Strong transcription	Fetal Stomach	stomach
45	chr19:35750600-35755800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr19:35751000-35753200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:35751000-35755200	Weak transcription	Colonic Mucosa	Colon
48	chr19:35751600-35753600	Enhancers	Brain Angular Gyrus	brain
49	chr19:35751800-35753400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:35751800-35753600	Enhancers	Brain Inferior Temporal Lobe	brain

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