Variant report

Variant	rs28654875
Chromosome Location	chr14:65770913-65770914
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	IKZF1	chr14:65769448-65770964	GM12878	blood:	n/a	n/a
2	EBF1	chr14:65770849-65771329	GM12878	blood:	n/a	n/a
3	POLR2A	chr14:65768458-65771398	GM12891	blood:	n/a	n/a
4	POLR2A	chr14:65768469-65771325	GM18951	blood:	n/a	n/a
5	POLR2A	chr14:65767150-65771470	GM12892	blood:	n/a	n/a
6	NFIC	chr14:65768050-65770972	GM12878	blood:	n/a	n/a
7	POLR2A	chr14:65767239-65771468	GM12892	blood:	n/a	n/a
8	POLR2A	chr14:65767525-65772793	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:65768350-65771408	GM12878	blood:	n/a	n/a
10	POLR2A	chr14:65767993-65772386	GM18505	blood:	n/a	n/a
11	RELA	chr14:65768445-65771188	GM12878	blood:	n/a	n/a
12	POLR2A	chr14:65767590-65772501	GM12892	blood:	n/a	n/a
13	POLR2A	chr14:65768552-65772630	Raji	blood:	n/a	n/a
14	POLR2A	chr14:65770642-65770986	GM12891	blood:	n/a	n/a
15	POLR2A	chr14:65767806-65771462	GM12892	blood:	n/a	n/a
16	NFATC1	chr14:65768356-65771125	GM12878	blood:	n/a	n/a
17	POLR2A	chr14:65768364-65771439	GM12891	blood:	n/a	n/a
18	RUNX3	chr14:65768306-65771264	GM12878	blood:	n/a	n/a
19	RELA	chr14:65768464-65771262	GM18505	blood:	n/a	n/a
20	STAT5A	chr14:65768360-65771354	GM12878	blood:	n/a	chr14:65769178-65769186 chr14:65771114-65771126
21	MTA3	chr14:65768424-65771359	GM12878	blood:	n/a	n/a
22	POLR2A	chr14:65770616-65771386	GM12892	blood:	n/a	n/a
23	BCLAF1	chr14:65768275-65771420	GM12878	blood:	n/a	chr14:65770652-65770665 chr14:65770644-65770657
24	POLR2A	chr14:65768385-65771394	GM19099	blood:	n/a	n/a
25	POLR2A	chr14:65768521-65771451	GM19193	blood:	n/a	n/a
26	RELA	chr14:65768429-65771360	GM19193	blood:	n/a	n/a
27	RELA	chr14:65768551-65771214	GM19099	blood:	n/a	n/a
28	POLR2A	chr14:65768067-65771238	GM12878	blood:	n/a	n/a
29	NFIC	chr14:65768506-65770959	GM12878	blood:	n/a	n/a
30	MAX	chr14:65770702-65771252	GM12878	blood:	n/a	n/a
31	MAZ	chr14:65768528-65771284	GM12878	blood:	n/a	n/a
32	EP300	chr14:65768607-65770956	GM12878	blood:	n/a	chr14:65770462-65770475 chr14:65769270-65769280
33	RELA	chr14:65768420-65771253	GM10847	blood:	n/a	n/a
34	ZNF384	chr14:65770878-65771397	GM12878	blood:	n/a	n/a
35	EBF1	chr14:65770857-65771360	GM12878	blood:	n/a	n/a
36	EP300	chr14:65768316-65771347	GM12878	blood:	n/a	chr14:65770462-65770475 chr14:65769270-65769280
37	TBL1XR1	chr14:65768350-65771067	GM12878	blood:	n/a	n/a
38	RELA	chr14:65768522-65771257	GM12891	blood:	n/a	n/a
39	POLR2A	chr14:65768397-65771443	GM12891	blood:	n/a	n/a
40	PML	chr14:65767561-65771290	GM12878	blood:	n/a	chr14:65770626-65770634
41	POLR2A	chr14:65768387-65771360	GM12878	blood:	n/a	n/a
42	RELA	chr14:65768591-65771216	GM15510	blood:	n/a	n/a
43	RUNX3	chr14:65768395-65771373	GM12878	blood:	n/a	n/a
44	POLR2A	chr14:65768430-65771381	GM15510	blood:	n/a	n/a
45	EBF1	chr14:65769279-65771249	GM12878	blood:	n/a	n/a
46	MTA3	chr14:65767857-65771465	GM12878	blood:	n/a	n/a
47	FOXM1	chr14:65768482-65771401	GM12878	blood:	n/a	n/a
48	POLR2A	chr14:65767278-65772457	GM12891	blood:	n/a	n/a
49	RELA	chr14:65768478-65771270	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65770511..65773505-chr14:65781617..65783190,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258760	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10047886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10130270	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10131095	0.89[AFR][1000 genomes]
rs10132304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10135430	0.89[AFR][1000 genomes]
rs10135555	0.89[AFR][1000 genomes]
rs10136600	0.89[AFR][1000 genomes]
rs10137961	0.89[AFR][1000 genomes]
rs10138521	0.89[AFR][1000 genomes]
rs10142126	0.89[AFR][1000 genomes]
rs10142520	0.89[AFR][1000 genomes]
rs10143378	0.89[AFR][1000 genomes]
rs10143537	0.89[AFR][1000 genomes]
rs10148449	0.89[AFR][1000 genomes]
rs10149224	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10150033	0.89[AFR][1000 genomes]
rs10150248	0.89[AFR][1000 genomes]
rs10150722	0.89[AFR][1000 genomes]
rs10151906	0.89[AFR][1000 genomes]
rs1679884	1.00[AMR][1000 genomes]
rs17102622	0.89[AFR][1000 genomes]
rs1871746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2152376	0.89[AFR][1000 genomes]
rs28425716	1.00[AMR][1000 genomes]
rs28438882	0.89[AFR][1000 genomes]
rs28459646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28462250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482071	0.89[AFR][1000 genomes]
rs28489429	0.89[AFR][1000 genomes]
rs28503629	1.00[AMR][1000 genomes]
rs28533687	1.00[AMR][1000 genomes]
rs28546829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28550810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583895	0.89[AFR][1000 genomes]
rs28591212	1.00[AMR][1000 genomes]
rs28649307	1.00[AMR][1000 genomes]
rs28649429	1.00[AMR][1000 genomes]
rs28708772	0.89[AFR][1000 genomes]
rs9323458	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832817	chr14:65637069-65810406	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv515522	chr14:65746566-65771110	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65758800-65773400	Weak transcription	Spleen	Spleen
2	chr14:65760000-65781000	Weak transcription	Primary B cells from cord blood	blood
3	chr14:65763200-65774200	Enhancers	Primary B cells from peripheral blood	blood
4	chr14:65763800-65771200	Enhancers	Fetal Intestine Small	intestine
5	chr14:65766000-65771200	Enhancers	Fetal Intestine Large	intestine
6	chr14:65766000-65772400	Enhancers	Stomach Mucosa	stomach
7	chr14:65766600-65771200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr14:65767600-65772800	Enhancers	Duodenum Mucosa	Duodenum
9	chr14:65768400-65772400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr14:65768400-65772800	Enhancers	Primary T cells from cord blood	blood
11	chr14:65768600-65771200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr14:65768600-65771200	Enhancers	Pancreas	Pancrea
13	chr14:65768600-65771400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr14:65768600-65772000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr14:65768600-65772400	Enhancers	Fetal Thymus	thymus
16	chr14:65768600-65772800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr14:65768600-65773600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr14:65768800-65771000	Enhancers	Fetal Stomach	stomach
19	chr14:65768800-65771200	Enhancers	Brain Hippocampus Middle	brain
20	chr14:65768800-65771200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr14:65768800-65771200	Enhancers	Hela-S3	cervix
22	chr14:65768800-65772000	Enhancers	Brain Substantia Nigra	brain
23	chr14:65768800-65772200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr14:65769000-65771000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:65769000-65771200	Enhancers	Brain Angular Gyrus	brain
26	chr14:65769000-65772400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr14:65769200-65771000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr14:65769200-65771000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:65769200-65771200	Enhancers	Brain Cingulate Gyrus	brain
30	chr14:65769200-65771200	Enhancers	Stomach Smooth Muscle	stomach
31	chr14:65769200-65772000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:65769200-65772000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr14:65769200-65772400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:65769200-65782400	Weak transcription	Gastric	stomach
35	chr14:65769400-65783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr14:65769800-65771000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr14:65769800-65771200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr14:65769800-65771200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr14:65769800-65771400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr14:65769800-65771400	Flanking Active TSS	GM12878-XiMat	blood
41	chr14:65769800-65771400	Enhancers	HepG2	liver
42	chr14:65770000-65771000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr14:65770000-65771000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr14:65770000-65771000	Weak transcription	HSMM	muscle
45	chr14:65770000-65771000	Enhancers	NHEK	skin
46	chr14:65770000-65771200	Enhancers	NH-A	brain
47	chr14:65770200-65771000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr14:65770200-65771000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr14:65770200-65771000	Enhancers	HSMMtube	muscle
50	chr14:65770200-65771200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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