Variant report

Variant	rs12461853
Chromosome Location	chr19:39005562-39005563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38892337..38894433-chr19:39004438..39006164,2	K562	blood:
2	chr19:39005438..39006386-chr19:39124743..39126011,6	K562	blood:
3	chr19:38969331..38969834-chr19:39005500..39006451,2	MCF-7	breast:
4	chr19:39005429..39005970-chr19:39378084..39378738,2	MCF-7	breast:
5	chr19:39004430..39007392-chr19:39334905..39337825,2	K562	blood:
6	chr19:39005491..39006744-chr19:39124980..39125890,3	MCF-7	breast:
7	chr19:39005451..39006360-chr19:39420704..39421428,2	MCF-7	breast:
8	chr19:39005447..39006042-chr19:39443307..39443821,2	MCF-7	breast:
9	chr19:39005418..39006382-chr19:39125015..39125812,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128626	Chromatin interaction
ENSG00000269190	Chromatin interaction
ENSG00000269688	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000130244	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1002072	1.00[AMR][1000 genomes]
rs12462002	0.81[AMR][1000 genomes]
rs1465698	1.00[AMR][1000 genomes]
rs3745851	1.00[AMR][1000 genomes]
rs3745852	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv911666	chr19:38948356-39014184	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38934800-39005600	Strong transcription	Fetal Muscle Leg	muscle
2	chr19:38940000-39006400	Weak transcription	HSMM	muscle
3	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
5	chr19:38981600-39005600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:38982200-39005600	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
8	chr19:38996200-39007800	Weak transcription	Right Atrium	heart
9	chr19:38997600-39007000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:38997600-39025400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:38997800-39005600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:38998400-39005600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:38998600-39025000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:39000000-39013400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:39001000-39025600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:39001600-39007200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:39003200-39005600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:39003200-39006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:39003400-39005600	Weak transcription	Adipose Nuclei	Adipose
20	chr19:39003400-39006600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:39004400-39006400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr19:39004600-39006400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr19:39005200-39006400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:39005200-39006400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:39005200-39006800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:39005200-39006800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr19:39005200-39008200	Strong transcription	HSMMtube	muscle
28	chr19:39005400-39005600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr19:39005400-39005600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:39005400-39005800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39005400-39005800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:39005400-39005800	Flanking Active TSS	A549	lung
33	chr19:39005400-39005800	Enhancers	HepG2	liver
34	chr19:39005400-39006200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr19:39005400-39006200	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:39005400-39006200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:39005400-39006200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39005400-39006200	Enhancers	Brain Angular Gyrus	brain
39	chr19:39005400-39006200	Enhancers	Pancreas	Pancrea
40	chr19:39005400-39006200	Enhancers	GM12878-XiMat	blood
41	chr19:39005400-39006400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr19:39005400-39006400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39005400-39006400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:39005400-39006400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr19:39005400-39006400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr19:39005400-39006600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr19:39005400-39006600	Enhancers	Brain Anterior Caudate	brain
48	chr19:39005400-39006600	Enhancers	K562	blood
49	chr19:39005400-39006800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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