Variant report

Variant	rs12460771
Chromosome Location	chr19:45657683-45657684
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	chr19:45657601-45657941	HepG2	liver:	n/a	n/a
2	ARID3A	chr19:45657629-45658022	HepG2	liver:	n/a	n/a
3	RCOR1	chr19:45657584-45658171	K562	blood:	n/a	n/a
4	SMC3	chr19:45657654-45657878	HepG2	liver:	n/a	n/a
5	CTCF	chr19:45657680-45657830	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr19:45657680-45657830	HEEpiC	esophagus:	n/a	n/a
7	CTCF	chr19:45657540-45657690	GM06990	blood:	n/a	n/a
8	POLR2A	chr19:45656816-45658087	PFSK-1	brain:	n/a	n/a
9	FOXA1	chr19:45657221-45657774	HepG2	liver:	n/a	n/a
10	NFYA	chr19:45657636-45658013	Hela-S3	cervix:	n/a	n/a
11	GTF2F1	chr19:45657665-45658005	Hela-S3	cervix:	n/a	n/a
12	TCF7L2	chr19:45657572-45658206	Hela-S3	cervix:	n/a	chr19:45657980-45657989 chr19:45657977-45657993
13	POLR2A	chr19:45657625-45657880	HepG2	liver:	n/a	n/a
14	MAX	chr19:45656651-45658096	HepG2	liver:	n/a	chr19:45657081-45657091 chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945
15	ELK1	chr19:45657573-45657842	K562	blood:	n/a	n/a
16	NR3C1	chr19:45657421-45658088	A549	lung:	n/a	chr19:45657768-45657794 chr19:45657774-45657788 chr19:45657772-45657790 chr19:45657768-45657794 chr19:45657770-45657791 chr19:45657829-45657842 chr19:45657768-45657794 chr19:45657781-45657788 chr19:45657768-45657794 chr19:45657768-45657794
17	POLR2A	chr19:45657171-45658145	HepG2	liver:	n/a	n/a
18	USF2	chr19:45657589-45658142	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr19:45657640-45657790	HPAF	blood vessel:	n/a	n/a
20	TBL1XR1	chr19:45657674-45657684	K562	blood:	n/a	n/a
21	EP300	chr19:45657317-45658122	HepG2	liver:	n/a	chr19:45657753-45657769
22	POLR2A	chr19:45657566-45657980	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr19:45657640-45657790	HCPEpiC	choroid plexus:	n/a	n/a
24	SMC3	chr19:45657608-45657892	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr19:45657604-45657821	HepG2	liver:	n/a	n/a
26	CTCF	chr19:45657540-45657690	HCM	heart:	n/a	n/a
27	CTCF	chr19:45657620-45657770	AG04450	lung:	n/a	n/a
28	TCF7L2	chr19:45657592-45658040	HepG2	liver:	n/a	chr19:45657980-45657989 chr19:45657977-45657993
29	CTCF	chr19:45657640-45657790	HEK293	kidney:	n/a	n/a
30	POLR2A	chr19:45657325-45657725	H1-neurons	neurons:	n/a	n/a
31	FOXA1	chr19:45657157-45658083	HepG2	liver:	n/a	n/a
32	CTCF	chr19:45657660-45657810	HEEpiC	esophagus:	n/a	n/a
33	CTCF	chr19:45657680-45657830	AG04449	skin:	n/a	n/a
34	CTCF	chr19:45657580-45657730	Hela-S3	cervix:	n/a	n/a
35	HEY1	chr19:45657522-45657866	HepG2	liver:	n/a	n/a
36	CTCF	chr19:45657660-45657810	HRE	kidney:	n/a	n/a
37	POLR2A	chr19:45657623-45657989	Hela-S3	cervix:	n/a	n/a
38	MAZ	chr19:45657029-45658052	K562	blood:	n/a	chr19:45657081-45657091 chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945
39	NR3C1	chr19:45657318-45658248	A549	lung:	n/a	chr19:45657768-45657794 chr19:45657774-45657788 chr19:45657772-45657790 chr19:45657768-45657794 chr19:45657770-45657791 chr19:45657829-45657842 chr19:45657768-45657794 chr19:45657781-45657788 chr19:45657768-45657794 chr19:45657768-45657794
40	CTCF	chr19:45657640-45657790	AG10803	skin:	n/a	n/a
41	EGR1	chr19:45657008-45658316	HCT-116	colon:	n/a	chr19:45657203-45657212 chr19:45657200-45657213 chr19:45657200-45657213 chr19:45657200-45657214 chr19:45657200-45657213 chr19:45657199-45657214 chr19:45657080-45657090 chr19:45657081-45657091 chr19:45657201-45657212 chr19:45657200-45657213 chr19:45657202-45657212 chr19:45657202-45657212 chr19:45657076-45657089
42	JUN	chr19:45656734-45658282	K562	blood:	n/a	n/a
43	SP1	chr19:45657326-45658084	HepG2	liver:	n/a	chr19:45657353-45657367
44	POLR2A	chr19:45657666-45658096	HCT-116	colon:	n/a	n/a
45	FOXA1	chr19:45657251-45657759	HepG2	liver:	n/a	n/a
46	CUX1	chr19:45657543-45657805	K562	blood:	n/a	n/a
47	MXI1	chr19:45654849-45658095	IMR90	lung:	n/a	chr19:45657939-45657948 chr19:45657937-45657946
48	KAP1	chr19:45656669-45657984	HEK293	kidney:	n/a	n/a
49	MYC	chr19:45657372-45658164	K562	blood:	n/a	chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945
50	CTCF	chr19:45657640-45657790	HMF	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45651718..45653898-chr19:45656029..45658572,2	K562	blood:
2	chr19:45646614..45649721-chr19:45656300..45659382,4	K562	blood:
3	chr19:45654421..45658397-chr19:45679888..45682724,3	K562	blood:
4	chr19:45640971..45644367-chr19:45655076..45659170,3	K562	blood:

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000267037	TF binding region
ENSG00000189114	Chromatin interaction
ENSG00000267037	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10420443	1.00[AMR][1000 genomes]
rs12459851	1.00[AMR][1000 genomes]
rs12460007	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45651800-45660200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:45654600-45658000	Bivalent Enhancer	Placenta	Placenta
3	chr19:45654800-45660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:45655200-45658000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:45656000-45658000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
6	chr19:45656200-45657800	Enhancers	Gastric	stomach
7	chr19:45656400-45657800	Enhancers	Lung	lung
8	chr19:45656400-45658000	Bivalent Enhancer	Fetal Thymus	thymus
9	chr19:45656400-45658000	Bivalent Enhancer	Spleen	Spleen
10	chr19:45656400-45658000	Bivalent Enhancer	NHDF-Ad	bronchial
11	chr19:45656600-45657800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:45656600-45658000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:45656800-45657800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr19:45656800-45657800	Bivalent Enhancer	Stomach Mucosa	stomach
15	chr19:45656800-45658000	Enhancers	HMEC	breast
16	chr19:45656800-45658000	Enhancers	HUVEC	blood vessel
17	chr19:45657000-45657800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr19:45657000-45657800	Enhancers	Pancreas	Pancrea
19	chr19:45657000-45657800	Bivalent Enhancer	GM12878-XiMat	blood
20	chr19:45657000-45658000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:45657000-45658000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
22	chr19:45657000-45658000	Enhancers	Esophagus	oesophagus
23	chr19:45657000-45658000	Enhancers	HSMM	muscle
24	chr19:45657000-45658000	Flanking Active TSS	K562	blood
25	chr19:45657000-45658000	Enhancers	NHLF	lung
26	chr19:45657000-45658200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:45657000-45658200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr19:45657200-45657800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:45657200-45657800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr19:45657200-45657800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
31	chr19:45657200-45658000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:45657200-45658000	Enhancers	Right Ventricle	heart
33	chr19:45657200-45658000	Enhancers	A549	lung
34	chr19:45657200-45658000	Flanking Active TSS	Hela-S3	cervix
35	chr19:45657200-45658000	Flanking Active TSS	HepG2	liver
36	chr19:45657400-45657800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:45657400-45657800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr19:45657400-45657800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:45657400-45657800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:45657400-45657800	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr19:45657400-45657800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr19:45657400-45657800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
43	chr19:45657400-45657800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:45657400-45657800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:45657400-45657800	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr19:45657400-45657800	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr19:45657400-45657800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr19:45657400-45657800	Bivalent Enhancer	Fetal Stomach	stomach
49	chr19:45657400-45657800	Enhancers	Ovary	ovary
50	chr19:45657400-45657800	Enhancers	Right Atrium	heart

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