Variant report

Variant	rs3212858
Chromosome Location	chr19:51321953-51321954
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:6)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51314145..51316152-chr19:51321518..51323994,2	MCF-7	breast:
2	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
3	chr19:51316544..51318313-chr19:51321412..51323624,2	K562	blood:
4	chr19:51317914..51322870-chr19:51325257..51328084,4	MCF-7	breast:
5	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:
6	chr19:51321294..51329149-chr19:51334672..51341529,13	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC010325.1-1	chr19:51321483-51322108	XLOC_013119
2	lnc-AC010325.1-1	chr19:51321486-51322105	XLOC_013119
3	lnc-AC010325.1-1	chr19:51321483-51322108	XLOC_013119
4	lnc-AC010325.1-1	chr19:51321391-51322133	XLOC_013119
5	lnc-AC010325.1-1	chr19:51321391-51322134	ENSG00000180279.5

No data

Variant related genes	Relation type
ENSG00000167748	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000167747	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10421200	1.00[EUR][1000 genomes]
rs3212808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212814	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212815	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212829	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212842	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212844	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3212847	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36217621	0.96[EUR][1000 genomes]
rs5514	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5515	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7259922	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv516450	chr19:51321083-51322312	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv524637	chr19:51321083-51332670	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv523089	chr19:51321083-51336197	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51320600-51322000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:51320800-51338800	Weak transcription	Right Atrium	heart
3	chr19:51321000-51322000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:51321000-51322000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:51321000-51322000	Flanking Active TSS	HMEC	breast
6	chr19:51321000-51322200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:51321000-51322200	Bivalent Enhancer	Spleen	Spleen
8	chr19:51321200-51322000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr19:51321200-51322000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:51321200-51322000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:51321200-51322000	Enhancers	Gastric	stomach
12	chr19:51321200-51322000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr19:51321200-51322600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:51321400-51322000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:51321400-51322000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:51321400-51322000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:51321400-51322000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
18	chr19:51321400-51322000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:51321400-51322000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:51321400-51322000	Bivalent Enhancer	Liver	Liver
21	chr19:51321400-51322000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr19:51321400-51322000	Enhancers	Lung	lung
23	chr19:51321400-51322000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr19:51321400-51322000	Bivalent/Poised TSS	HSMM	muscle
25	chr19:51321400-51322000	Bivalent/Poised TSS	Osteobl	bone
26	chr19:51321400-51322200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:51321400-51322200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
28	chr19:51321400-51322200	Bivalent Enhancer	Right Ventricle	heart
29	chr19:51321400-51322400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
30	chr19:51321400-51322400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr19:51321400-51322800	Flanking Active TSS	Pancreas	Pancrea
32	chr19:51321400-51324000	Flanking Active TSS	GM12878-XiMat	blood
33	chr19:51321600-51322000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:51321600-51322000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:51321600-51322000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:51321600-51322000	Bivalent Enhancer	Left Ventricle	heart
37	chr19:51321600-51322200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr19:51321600-51322200	Bivalent Enhancer	Placenta	Placenta
39	chr19:51321600-51322200	Flanking Active TSS	K562	blood
40	chr19:51321600-51322400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr19:51321600-51322400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
42	chr19:51321600-51322400	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr19:51321800-51322000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr19:51321800-51322000	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:51321800-51322000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
46	chr19:51321800-51322000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
47	chr19:51321800-51322000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
48	chr19:51321800-51322000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:51321800-51322000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
50	chr19:51321800-51322000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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