Variant report

Variant	rs10424609
Chromosome Location	chr19:55678906-55678907
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	RCOR1	chr19:55677348-55679357	Hela-S3	cervix:	n/a	n/a
2	HA-E2F1	chr19:55678091-55678975	MCF-7	breast:	n/a	chr19:55678165-55678174
3	MAX	chr19:55677114-55678906	A549	lung:	n/a	n/a
4	CEBPB	chr19:55678107-55678906	A549	lung:	n/a	chr19:55678315-55678332
5	TCF12	chr19:55677159-55678932	A549	lung:	n/a	n/a
6	SMARCC2	chr19:55678145-55679382	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr19:55676755-55678947	A549	lung:	n/a	chr19:55677561-55677574
8	SIN3AK20	chr19:55677126-55678953	MCF-7	breast:	n/a	n/a
9	MAX	chr19:55677405-55679241	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr19:55677369-55679284	Hela-S3	cervix:	n/a	chr19:55677561-55677575
11	HCFC1	chr19:55676917-55678968	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:55677219-55678971	K562	blood:	n/a	n/a
13	CEBPB	chr19:55678237-55678954	A549	lung:	n/a	chr19:55678315-55678332
14	POLR2A	chr19:55676946-55679044	PFSK-1	brain:	n/a	n/a
15	ZNF384	chr19:55678238-55679267	K562	blood:	n/a	n/a
16	SP1	chr19:55676937-55678919	HCT-116	colon:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677063-55677077 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838

No.	Distal block	Cell Line	Cell type
1	chr19:55678413..55680663-chr19:55987630..55990002,2	MCF-7	breast:
2	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
3	chr19:55677411..55679148-chr19:55895317..55896952,2	MCF-7	breast:
4	chr19:55677572..55679137-chr19:55970708..55972707,2	K562	blood:
5	chr19:55676191..55679387-chr19:55917452..55919839,3	K562	blood:
6	chr19:55676374..55679520-chr19:55726674..55730754,4	K562	blood:
7	chr19:55592134..55595044-chr19:55674815..55678963,4	K562	blood:
8	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
9	chr19:55677235..55679036-chr19:55897209..55898733,2	K562	blood:
10	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
11	chr19:55677887..55680823-chr19:55918139..55920221,3	K562	blood:
12	chr19:55590129..55594149-chr19:55677127..55678963,3	K562	blood:

Variant related genes	Relation type
DNAAF3	TF binding region
ENSG00000197483	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000063241	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10424638	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670538	0.87[ASN][1000 genomes]
rs13343638	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16986289	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16986292	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16986294	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3729837	0.91[ASN][1000 genomes]
rs3729841	0.91[ASN][1000 genomes]
rs3859540	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3859542	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6509927	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6509930	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248799	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8107129	0.88[ASN][1000 genomes]
rs8107736	0.88[ASN][1000 genomes]
rs8110415	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9749340	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55677200-55679000	Enhancers	Spleen	Spleen
2	chr19:55677200-55679200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr19:55677400-55679000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr19:55677400-55679000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:55677400-55679000	Active TSS	A549	lung
6	chr19:55677400-55679200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr19:55677600-55679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:55677600-55679000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:55677600-55679200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
10	chr19:55677600-55679200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:55677800-55679000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:55677800-55679000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:55677800-55679000	Active TSS	Right Ventricle	heart
14	chr19:55678000-55679000	Enhancers	Pancreas	Pancrea
15	chr19:55678000-55679200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:55678000-55679200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
17	chr19:55678200-55679000	Weak transcription	Esophagus	oesophagus
18	chr19:55678200-55679000	Bivalent Enhancer	Placenta	Placenta
19	chr19:55678200-55679200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
20	chr19:55678200-55679200	Flanking Active TSS	NHEK	skin
21	chr19:55678200-55679400	Flanking Active TSS	Hela-S3	cervix
22	chr19:55678400-55679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:55678400-55679000	Flanking Active TSS	HepG2	liver
24	chr19:55678600-55679000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:55678600-55679000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr19:55678600-55679000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:55678600-55679000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr19:55678600-55679000	Bivalent Enhancer	Fetal Brain Male	brain
29	chr19:55678600-55679000	Bivalent Enhancer	Fetal Intestine Small	intestine
30	chr19:55678600-55679000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
31	chr19:55678600-55679000	Weak transcription	Right Atrium	heart
32	chr19:55678600-55679200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
33	chr19:55678600-55679400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
34	chr19:55678600-55679400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:55678600-55679400	Bivalent Enhancer	Liver	Liver
36	chr19:55678600-55679400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
37	chr19:55678800-55679000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr19:55678800-55679000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:55678800-55679000	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr19:55678800-55679000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:55678800-55679000	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr19:55678800-55679000	Active TSS	K562	blood
43	chr19:55678800-55679200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:55678800-55679200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
45	chr19:55678800-55679200	Bivalent Enhancer	Stomach Mucosa	stomach
46	chr19:55678800-55679400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:55678800-55679400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:55678800-55679400	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links