Variant report

Variant	rs6078926
Chromosome Location	chr20:13103161-13103162
allele	C/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	BCLAF1	chr20:13102770-13103175	GM12878	blood:	n/a	n/a
2	RUNX3	chr20:13102368-13103265	GM12878	blood:	n/a	n/a
3	BATF	chr20:13102428-13103193	GM12878	blood:	n/a	n/a
4	PAX5	chr20:13102701-13103234	GM12878	blood:	n/a	n/a
5	MTA3	chr20:13102353-13103232	GM12878	blood:	n/a	n/a
6	NFATC1	chr20:13102698-13103199	GM12878	blood:	n/a	n/a
7	RAD21	chr20:13102999-13103236	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFIC	chr20:13102349-13103324	GM12878	blood:	n/a	n/a
9	RELA	chr20:13102494-13103241	GM12891	blood:	n/a	n/a
10	EP300	chr20:13102582-13103165	GM12878	blood:	n/a	n/a
11	EP300	chr20:13101753-13103222	HepG2	liver:	n/a	chr20:13102071-13102084
12	STAT5A	chr20:13102709-13103172	GM12878	blood:	n/a	chr20:13102723-13102731
13	BATF	chr20:13102418-13103170	GM12878	blood:	n/a	n/a
14	IRF4	chr20:13102429-13103260	GM12878	blood:	n/a	n/a
15	TCF3	chr20:13102753-13103175	GM12878	blood:	n/a	n/a
16	SPI1	chr20:13102755-13103204	GM12891	blood:	n/a	chr20:13103005-13103018
17	MBD4	chr20:13102256-13103179	HepG2	liver:	n/a	n/a
18	BCLAF1	chr20:13102694-13103190	GM12878	blood:	n/a	n/a
19	FOXM1	chr20:13102433-13103229	GM12878	blood:	n/a	chr20:13102946-13102954
20	RUNX3	chr20:13102444-13103174	GM12878	blood:	n/a	n/a
21	EBF1	chr20:13102857-13103453	GM12878	blood:	n/a	chr20:13103340-13103351
22	SPI1	chr20:13102778-13103242	GM12878	blood:	n/a	chr20:13103005-13103018
23	RCOR1	chr20:13102878-13103204	GM12878	blood:	n/a	n/a
24	RELA	chr20:13102799-13103205	GM19099	blood:	n/a	n/a
25	SPI1	chr20:13102472-13103423	GM12878	blood:	n/a	chr20:13103005-13103018
26	SPI1	chr20:13102710-13103180	GM12891	blood:	n/a	chr20:13103005-13103018
27	RELA	chr20:13102797-13103179	GM19193	blood:	n/a	n/a
28	FOXM1	chr20:13102322-13103268	GM12878	blood:	n/a	chr20:13102946-13102954
29	WRNIP1	chr20:13103069-13103212	GM12878	blood:	n/a	n/a
30	ATF2	chr20:13102367-13103217	GM12878	blood:	n/a	n/a
31	IRF4	chr20:13102704-13103244	GM12878	blood:	n/a	n/a
32	RELA	chr20:13102476-13103167	GM12878	blood:	n/a	n/a
33	CTCF	chr20:13103079-13103175	GM19238	blood:	n/a	n/a
34	BCL11A	chr20:13102456-13103180	GM12878	blood:	n/a	n/a
35	ZNF143	chr20:13102743-13103268	GM12878	blood:	n/a	n/a
36	EP300	chr20:13102492-13103189	GM12878	blood:	n/a	n/a
37	NFATC1	chr20:13102436-13103219	GM12878	blood:	n/a	n/a
38	NFIC	chr20:13102281-13103342	GM12878	blood:	n/a	n/a
39	CEBPB	chr20:13102530-13103260	GM12878	blood:	n/a	n/a
40	PML	chr20:13102609-13103239	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13102577..13104430-chr20:13278483..13280151,2	MCF-7	breast:

Variant related genes	Relation type
SPTLC3	TF binding region

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13042895	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2180365	0.91[ASN][1000 genomes]
rs2208004	0.82[ASN][1000 genomes]
rs2236125	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236126	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2327752	0.91[ASN][1000 genomes]
rs2327753	0.91[ASN][1000 genomes]
rs35868902	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4274654	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6033620	0.90[ASN][1000 genomes]
rs6074558	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6074559	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6074560	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6078920	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6078922	0.89[ASN][1000 genomes]
rs6078925	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105040	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6109710	0.83[ASN][1000 genomes]
rs6109713	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109717	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
2	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
4	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:13086200-13107600	Weak transcription	NHEK	skin
6	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:13087800-13107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
10	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
11	chr20:13093200-13106800	Weak transcription	Ovary	ovary
12	chr20:13093400-13108000	Weak transcription	Aorta	Aorta
13	chr20:13093400-13111000	Weak transcription	Lung	lung
14	chr20:13094200-13103400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:13096600-13116600	Weak transcription	Right Ventricle	heart
17	chr20:13098400-13107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr20:13098600-13105200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr20:13100000-13103600	Genic enhancers	HepG2	liver
20	chr20:13100000-13108800	Weak transcription	Adipose Nuclei	Adipose
21	chr20:13101000-13110800	Weak transcription	Small Intestine	intestine
22	chr20:13101200-13106400	Strong transcription	Fetal Intestine Small	intestine
23	chr20:13101400-13104600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:13101600-13113600	Weak transcription	Fetal Stomach	stomach
25	chr20:13102000-13112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr20:13102200-13108400	Strong transcription	Liver	Liver
27	chr20:13102200-13111000	Strong transcription	Placenta	Placenta
28	chr20:13102400-13103200	Enhancers	GM12878-XiMat	blood
29	chr20:13102600-13103200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
30	chr20:13102800-13104200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr20:13102800-13106400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr20:13103000-13103800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links