Variant report

Variant	rs10424638
Chromosome Location	chr19:55679048-55679049
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:55678965-55679344	K562	blood:	n/a	n/a
2	CBX3	chr19:55678930-55679399	K562	blood:	n/a	n/a
3	MAX	chr19:55678943-55679330	K562	blood:	n/a	n/a
4	RCOR1	chr19:55677348-55679357	Hela-S3	cervix:	n/a	n/a
5	SMARCC2	chr19:55678145-55679382	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr19:55678989-55679292	K562	blood:	n/a	n/a
7	MAX	chr19:55677405-55679241	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr19:55677369-55679284	Hela-S3	cervix:	n/a	chr19:55677561-55677575
9	ZNF143	chr19:55679004-55679300	Hela-S3	cervix:	n/a	n/a
10	HDAC2	chr19:55678952-55679318	K562	blood:	n/a	chr19:55679187-55679206
11	ZNF384	chr19:55678238-55679267	K562	blood:	n/a	n/a
12	ZNF143	chr19:55679036-55679272	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

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	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
8	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
9	chr19:55677887..55680823-chr19:55918139..55920221,3	K562	blood:

No data

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10424609	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669300	0.88[ASN][1000 genomes]
rs11670538	0.96[ASN][1000 genomes]
rs11672000	0.88[ASN][1000 genomes]
rs11672834	0.88[ASN][1000 genomes]
rs12104158	0.85[AFR][1000 genomes]
rs13343638	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16986289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986294	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729837	1.00[ASN][1000 genomes]
rs3729841	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3859540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248799	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107129	0.96[ASN][1000 genomes]
rs8107736	0.96[ASN][1000 genomes]
rs8110415	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749340	0.96[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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55677200-55679200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr19:55677400-55679200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr19:55677600-55679200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
4	chr19:55677600-55679200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:55678000-55679200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:55678000-55679200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
7	chr19:55678200-55679200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
8	chr19:55678200-55679200	Flanking Active TSS	NHEK	skin
9	chr19:55678200-55679400	Flanking Active TSS	Hela-S3	cervix
10	chr19:55678600-55679200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr19:55678600-55679400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr19:55678600-55679400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:55678600-55679400	Bivalent Enhancer	Liver	Liver
14	chr19:55678600-55679400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr19:55678800-55679200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:55678800-55679200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
17	chr19:55678800-55679200	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr19:55678800-55679400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:55678800-55679400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:55678800-55679400	Enhancers	HMEC	breast
21	chr19:55679000-55679200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
22	chr19:55679000-55679200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:55679000-55679200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:55679000-55679200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:55679000-55679200	Enhancers	Right Atrium	heart
26	chr19:55679000-55679200	Flanking Active TSS	K562	blood
27	chr19:55679000-55679400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:55679000-55679400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
29	chr19:55679000-55679400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:55679000-55679400	Enhancers	Esophagus	oesophagus
31	chr19:55679000-55679400	Bivalent Enhancer	Spleen	Spleen
32	chr19:55679000-55679400	Flanking Active TSS	A549	lung
33	chr19:55679000-55684000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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