Variant report

Variant	rs28373835
Chromosome Location	chr14:56050942-56050943
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	CEBPB	chr14:56050926-56051252	A549	lung:	n/a	chr14:56051080-56051091
2	RCOR1	chr14:56050605-56050983	K562	blood:	n/a	n/a
3	CEBPB	chr14:56050893-56051269	HepG2	liver:	n/a	chr14:56051080-56051091
4	GATA3	chr14:56050454-56051092	SH-SY5Y	brain:	n/a	n/a
5	GATA2	chr14:56050433-56051230	SH-SY5Y	brain:	n/a	n/a
6	CEBPB	chr14:56050575-56051344	Hela-S3	cervix:	n/a	chr14:56051080-56051091
7	TCF7L2	chr14:56050538-56051238	HEK293	kidney:	n/a	n/a
8	GATA3	chr14:56050468-56051064	SK-N-SH	brain:	n/a	n/a
9	MAX	chr14:56050476-56051290	Hela-S3	cervix:	n/a	n/a
10	WRNIP1	chr14:56050479-56051019	GM12878	blood:	n/a	n/a
11	KAP1	chr14:56050493-56051465	U2OS	brain:	n/a	n/a
12	KAP1	chr14:56050300-56051476	HEK293	kidney:	n/a	n/a
13	CEBPB	chr14:56050895-56051272	IMR90	lung:	n/a	chr14:56051080-56051091
14	RCOR1	chr14:56050664-56051227	Hela-S3	cervix:	n/a	n/a
15	CCNT2	chr14:56050706-56051046	K562	blood:	n/a	n/a
16	CEBPB	chr14:56050910-56051265	K562	blood:	n/a	chr14:56051080-56051091
17	FOXA1	chr14:56050836-56051363	HepG2	liver:	n/a	n/a
18	POLR2A	chr14:56050308-56051496	HepG2	liver:	n/a	n/a
19	ZNF263	chr14:56050375-56051394	HEK293-T-REx	kidney:	n/a	n/a
20	FOXA1	chr14:56050859-56051239	HepG2	liver:	n/a	n/a
21	HDAC2	chr14:56050905-56051195	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:56050224..56053643-chr14:56057156..56060698,4	MCF-7	breast:
2	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:
3	chr14:56050702..56052550-chr14:56072121..56074340,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO34-2	chr14:56050822-56050988	ucscGeneNc_uc001xci_2

Variant related genes	Relation type
KTN1-AS1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10083493	0.82[AFR][1000 genomes]
rs10129537	1.00[AMR][1000 genomes]
rs10135124	1.00[AMR][1000 genomes]
rs10135509	1.00[EUR][1000 genomes]
rs10137340	0.86[AFR][1000 genomes]
rs10142497	0.82[AFR][1000 genomes]
rs10142757	0.94[AFR][1000 genomes]
rs10142869	1.00[AMR][1000 genomes]
rs10143002	0.91[AFR][1000 genomes]
rs10148188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10148983	0.94[AFR][1000 genomes]
rs13379264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13379340	0.86[AFR][1000 genomes]
rs13379342	0.94[AFR][1000 genomes]
rs13379343	0.88[AFR][1000 genomes]
rs13379353	0.86[AFR][1000 genomes]
rs17683656	0.94[AFR][1000 genomes]
rs28366673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28409547	0.80[AFR][1000 genomes]
rs28478195	0.82[AFR][1000 genomes]
rs28534706	1.00[EUR][1000 genomes]
rs28558467	1.00[EUR][1000 genomes]
rs28656140	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9944028	0.94[AFR][1000 genomes]
rs9972177	0.86[AFR][1000 genomes]
rs9972178	0.94[AFR][1000 genomes]
rs9972180	0.94[AFR][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	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56045600-56051000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:56048200-56054200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:56048400-56052000	Enhancers	Primary B cells from peripheral blood	blood
5	chr14:56048400-56052800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:56048400-56055200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr14:56048400-56056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
9	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:56048600-56051200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:56048600-56051200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr14:56048600-56051400	Enhancers	Primary hematopoietic stem cells	blood
13	chr14:56048600-56051400	Enhancers	Rectal Smooth Muscle	rectum
14	chr14:56048600-56051600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:56048600-56051600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr14:56048600-56052400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:56048600-56052400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr14:56048600-56052800	Weak transcription	Thymus	Thymus
19	chr14:56048600-56053000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:56048600-56053600	Enhancers	Osteobl	bone
21	chr14:56048600-56054000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr14:56048600-56055400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr14:56048600-56055400	Enhancers	Liver	Liver
24	chr14:56048600-56058400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:56048600-56060400	Weak transcription	Brain Substantia Nigra	brain
26	chr14:56048600-56070800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:56048800-56051000	Enhancers	NHDF-Ad	bronchial
28	chr14:56048800-56051200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:56048800-56051400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr14:56048800-56055000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr14:56049000-56051200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr14:56049000-56051200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr14:56049000-56051200	Enhancers	Dnd41	blood
34	chr14:56049000-56051800	Enhancers	HepG2	liver
35	chr14:56049000-56052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:56049200-56051600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:56049200-56051600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:56049200-56051600	Enhancers	Colon Smooth Muscle	Colon
39	chr14:56049200-56055200	Enhancers	Primary T cells from cord blood	blood
40	chr14:56049400-56051200	Enhancers	NHLF	lung
41	chr14:56049400-56051400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr14:56049400-56051600	Enhancers	HSMM	muscle
43	chr14:56049600-56051000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr14:56049600-56051200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:56049600-56051600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:56049600-56051800	Enhancers	Stomach Mucosa	stomach
47	chr14:56049600-56052000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:56049600-56052000	Weak transcription	HUVEC	blood vessel
49	chr14:56049600-56052400	Enhancers	HSMMtube	muscle
50	chr14:56049600-56053000	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links