Variant report

Variant	rs12459061
Chromosome Location	chr19:40789415-40789416
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	POLR2A	chr19:40789333-40791875	GM12878	blood:	n/a	n/a
2	CEBPB	chr19:40789312-40789807	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:40788968-40790490	HepG2	liver:	n/a	n/a
4	FOXA1	chr19:40789319-40790054	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:40789296-40790059	HepG2	liver:	n/a	n/a
6	CTCF	chr19:40789340-40789490	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:40788195-40792187	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr19:40789385-40791876	GM12878	blood:	n/a	n/a
9	HNF4A	chr19:40789325-40789921	HepG2	liver:	n/a	chr19:40789514-40789527 chr19:40789516-40789538 chr19:40789513-40789527 chr19:40789514-40789526 chr19:40789512-40789527
10	HCFC1	chr19:40789373-40789465	K562	blood:	n/a	n/a
11	POLR2A	chr19:40788136-40791242	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:40789056-40790872	GM12892	blood:	n/a	n/a
13	HNF4A	chr19:40789268-40789748	HepG2	liver:	n/a	chr19:40789514-40789527 chr19:40789516-40789538 chr19:40789513-40789527 chr19:40789514-40789526 chr19:40789512-40789527
14	MAZ	chr19:40789291-40789949	HepG2	liver:	n/a	n/a
15	FOXA1	chr19:40789397-40789974	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:40789377-40789961	HepG2	liver:	n/a	n/a
17	ZNF263	chr19:40789127-40790796	HEK293-T-REx	kidney:	n/a	chr19:40789676-40789685
18	HDAC2	chr19:40789332-40789842	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:40789062-40789989	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:40789129-40789524	K562	blood:	n/a	n/a
21	HNF4G	chr19:40789239-40789790	HepG2	liver:	n/a	chr19:40789514-40789527 chr19:40789516-40789538 chr19:40789511-40789526 chr19:40789513-40789527 chr19:40789514-40789526
22	POLR2A	chr19:40788900-40790001	K562	blood:	n/a	n/a
23	HEY1	chr19:40789285-40789928	K562	blood:	n/a	n/a
24	POLR2A	chr19:40789317-40790015	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:40789282-40789983	GM12878	blood:	n/a	n/a
26	HNF4A	chr19:40789293-40789909	HepG2	liver:	n/a	chr19:40789514-40789527 chr19:40789516-40789538 chr19:40789513-40789527 chr19:40789514-40789526 chr19:40789512-40789527
27	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr19:40789144-40792048	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:40787276-40792053	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:40789235-40791994	GM12892	blood:	n/a	n/a
31	ARID3A	chr19:40789369-40789589	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:40789313-40790066	HepG2	liver:	n/a	n/a
33	HNF4G	chr19:40789325-40789696	HepG2	liver:	n/a	chr19:40789514-40789527 chr19:40789516-40789538 chr19:40789511-40789526 chr19:40789513-40789527 chr19:40789514-40789526
34	RAD21	chr19:40789261-40789630	HepG2	liver:	n/a	n/a
35	POLR2A	chr19:40789156-40790050	K562	blood:	n/a	n/a
36	RXRA	chr19:40789260-40789725	HepG2	liver:	n/a	chr19:40789539-40789550 chr19:40789536-40789545 chr19:40789694-40789713 chr19:40789538-40789551 chr19:40789538-40789551
37	POLR2A	chr19:40789380-40789730	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:40789238-40789975	HepG2	liver:	n/a	n/a
39	HEY1	chr19:40789326-40789658	HepG2	liver:	n/a	n/a
40	ESRRA	chr19:40789302-40789725	HepG2	liver:	n/a	chr19:40789526-40789544 chr19:40789533-40789549 chr19:40789533-40789545 chr19:40789535-40789545 chr19:40789535-40789545
41	POLR2A	chr19:40789051-40791950	K562	blood:	n/a	n/a
42	SIN3AK20	chr19:40787407-40793117	PANC-1	pancreas:	n/a	n/a
43	CTCF	chr19:40789320-40789470	GM12875	blood:	n/a	n/a
44	SREBP1	chr19:40789027-40792196	GM12878	blood:	n/a	n/a
45	EP300	chr19:40789395-40789934	HepG2	liver:	n/a	chr19:40789594-40789610
46	POLR2A	chr19:40789272-40791877	GM19193	blood:	n/a	n/a
47	POLR2A	chr19:40789242-40791248	GM12891	blood:	n/a	n/a
48	WRNIP1	chr19:40788882-40789546	GM12878	blood:	n/a	n/a
49	TBP	chr19:40789414-40789903	HepG2	liver:	n/a	n/a
50	RCOR1	chr19:40789224-40789954	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40695407..40698481-chr19:40788292..40792778,5	K562	blood:
2	chr19:40787579..40789839-chr19:40846986..40849835,2	MCF-7	breast:
3	chr19:40788680..40791212-chr19:40852795..40854366,2	K562	blood:

Variant related genes	Relation type
MIR641	TF binding region
AKT2	TF binding region
ENSG00000206925	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000160392	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10281	1.00[CHD][hapmap]
rs8111547	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised 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	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
6	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
5	chr19:40779400-40789600	Enhancers	Left Ventricle	heart
6	chr19:40779800-40789800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:40783000-40789600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr19:40783400-40790000	Enhancers	Right Atrium	heart
9	chr19:40783800-40790600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:40785200-40789600	Genic enhancers	Fetal Intestine Small	intestine
11	chr19:40785800-40789600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr19:40785800-40789600	Genic enhancers	Fetal Stomach	stomach
13	chr19:40786000-40790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:40786400-40789600	Enhancers	Colon Smooth Muscle	Colon
15	chr19:40786400-40790200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:40786800-40789800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:40787000-40789600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:40787000-40789600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:40787000-40789600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:40787000-40790000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr19:40787000-40790000	Genic enhancers	Spleen	Spleen
22	chr19:40787200-40789600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:40787200-40789800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:40787200-40790000	Weak transcription	Small Intestine	intestine
25	chr19:40787600-40789800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:40787800-40789600	Genic enhancers	Primary T cells from cord blood	blood
27	chr19:40787800-40789800	Enhancers	Fetal Heart	heart
28	chr19:40787800-40790400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr19:40788000-40789800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr19:40788000-40789800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:40788400-40789600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:40788400-40789600	Enhancers	Right Ventricle	heart
33	chr19:40788400-40790000	Enhancers	Gastric	stomach
34	chr19:40788400-40790200	Enhancers	Esophagus	oesophagus
35	chr19:40788600-40789600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr19:40788600-40789600	Enhancers	Fetal Lung	lung
37	chr19:40788600-40789600	Enhancers	Pancreas	Pancrea
38	chr19:40788600-40789800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:40788600-40789800	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:40788600-40789800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:40788600-40789800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:40788600-40790200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:40788800-40789600	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:40788800-40789600	Enhancers	Fetal Intestine Large	intestine
45	chr19:40788800-40789600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:40788800-40789600	Flanking Active TSS	HepG2	liver
47	chr19:40788800-40789600	Enhancers	HMEC	breast
48	chr19:40788800-40789600	Enhancers	NH-A	brain
49	chr19:40788800-40789800	Enhancers	Fetal Kidney	kidney
50	chr19:40788800-40790000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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