Variant report

Variant	rs11882681
Chromosome Location	chr19:36426519-36426520
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	MAX	chr19:36426513-36427735	A549	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
2	REST	chr19:36426518-36428374	H1-neurons	neurons:	n/a	chr19:36426848-36426858 chr19:36427881-36427891
3	MXI1	chr19:36426391-36428778	SK-N-SH	brain:	n/a	n/a
4	MAZ	chr19:36426386-36427799	IMR90	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431

No.	Distal block	Cell Line	Cell type
1	chr19:36231818..36233362-chr19:36425701..36428426,2	MCF-7	breast:
2	chr19:36239375..36241509-chr19:36425781..36428099,2	MCF-7	breast:
3	chr19:36370775..36373541-chr19:36425672..36427378,2	MCF-7	breast:
4	chr19:36390062..36392033-chr19:36425677..36427196,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRFN3-1	chr19:36426260-36426684	NONHSAT065939

Variant related genes	Relation type
LRFN3	TF binding region
ENSG00000267796	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000126246	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11878548	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11879200	1.00[AMR][1000 genomes]
rs11879510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880514	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11881380	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11881594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11882484	1.00[AMR][1000 genomes]
rs11882893	0.86[AFR][1000 genomes]
rs14715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36422200-36426600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:36422400-36426600	Weak transcription	Liver	Liver
3	chr19:36422400-36426600	Weak transcription	Fetal Kidney	kidney
4	chr19:36422400-36426600	Weak transcription	HSMM	muscle
5	chr19:36423000-36426600	Weak transcription	Right Atrium	heart
6	chr19:36423000-36426600	Weak transcription	Spleen	Spleen
7	chr19:36423000-36426600	Weak transcription	HSMMtube	muscle
8	chr19:36423200-36426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36423200-36426600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:36423200-36426600	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:36423200-36426600	Weak transcription	Fetal Heart	heart
12	chr19:36423200-36426600	Weak transcription	GM12878-XiMat	blood
13	chr19:36423200-36426600	Weak transcription	HMEC	breast
14	chr19:36423200-36426600	Weak transcription	HUVEC	blood vessel
15	chr19:36423400-36426600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:36423400-36426600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:36423600-36426600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:36423600-36426600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:36423600-36426600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:36423800-36426600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:36423800-36426600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:36425600-36426800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:36425800-36426600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr19:36425800-36426600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr19:36426000-36426600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:36426000-36426600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:36426000-36426600	Enhancers	Primary T cells from cord blood	blood
28	chr19:36426000-36426600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:36426000-36426600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr19:36426000-36426600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:36426000-36426600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr19:36426000-36426600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:36426000-36426600	Enhancers	Fetal Brain Male	brain
34	chr19:36426000-36426600	Enhancers	Fetal Intestine Small	intestine
35	chr19:36426000-36426600	Enhancers	Fetal Muscle Trunk	muscle
36	chr19:36426000-36426600	Enhancers	Pancreas	Pancrea
37	chr19:36426000-36426800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:36426000-36426800	Enhancers	Gastric	stomach
39	chr19:36426000-36427000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:36426000-36427200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr19:36426200-36426600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:36426200-36426600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:36426200-36426600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36426200-36426600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:36426200-36426600	Active TSS	Brain Cingulate Gyrus	brain
46	chr19:36426200-36426600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:36426200-36426600	Enhancers	Fetal Stomach	stomach
48	chr19:36426200-36426600	Enhancers	Left Ventricle	heart
49	chr19:36426200-36426600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr19:36426200-36426600	Enhancers	NHLF	lung

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