Variant report

Variant	rs7255173
Chromosome Location	chr19:40474765-40474766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40472172-40495393	PANC-1	pancreas:	n/a	n/a
2	SIN3AK20	chr19:40473718-40478635	PANC-1	pancreas:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40324934..40327706-chr19:40474760..40476442,2	K562	blood:
2	chr19:40472468..40476413-chr19:40479730..40482224,3	MCF-7	breast:
3	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:
4	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
5	chr19:40473843..40476809-chr19:40580140..40582711,2	K562	blood:
6	chr19:40461619..40464271-chr19:40474236..40476089,2	K562	blood:
7	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:

No data

Variant related genes	Relation type
PSMC4	TF binding region
ENSG00000187187	Chromatin interaction
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16973959	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173062	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234335	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	1.00[ASN][1000 genomes]
rs234337	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234344	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234347	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234348	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234362	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234363	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234366	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234369	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234373	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542325	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2542328	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376630	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378554	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512360	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025633	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413463	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249398	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:40460200-40474800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:40460800-40476000	Weak transcription	Psoas Muscle	Psoas
4	chr19:40461600-40475400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:40464000-40475000	Weak transcription	GM12878-XiMat	blood
6	chr19:40466200-40476200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:40466400-40474800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:40466400-40474800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:40468600-40475600	Weak transcription	Brain Anterior Caudate	brain
10	chr19:40470000-40475200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr19:40470200-40475200	Weak transcription	Stomach Mucosa	stomach
12	chr19:40471800-40475200	Weak transcription	A549	lung
13	chr19:40472600-40475400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:40472600-40475600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:40472800-40476000	Weak transcription	Brain Angular Gyrus	brain
16	chr19:40473000-40475000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:40473000-40476000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:40473000-40476000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:40473400-40475400	Enhancers	Primary T cells from cord blood	blood
20	chr19:40474000-40475000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr19:40474000-40476200	Weak transcription	Fetal Kidney	kidney
22	chr19:40474000-40476200	Enhancers	HepG2	liver
23	chr19:40474200-40475600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:40474200-40476200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:40474400-40474800	Weak transcription	Fetal Intestine Small	intestine
26	chr19:40474400-40476000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr19:40474600-40476000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links