Variant report

Variant	rs12086328
Chromosome Location	chr1:144607401-144607402
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL592284.1-1	chr1:144607095-144607547	ENSG00000225241

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11261220	0.89[AFR][1000 genomes]
rs3009747	0.83[EUR][1000 genomes]
rs3009751	0.84[EUR][1000 genomes]
rs9727633	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012104	chr1:144007818-144682096	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	260 gene(s)	inside rSNPs	diseases
2	nsv1006330	chr1:144007818-144849544	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	262 gene(s)	inside rSNPs	diseases
3	nsv1001989	chr1:144007818-144873327	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
4	nsv997949	chr1:144007818-144876884	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
5	nsv1010670	chr1:144007818-144880405	Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
6	nsv1010163	chr1:144007818-144884322	Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
7	nsv1014985	chr1:144007818-144949963	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv1002373	chr1:144013582-144682096	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	258 gene(s)	inside rSNPs	diseases
9	nsv1007748	chr1:144015838-144682096	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	258 gene(s)	inside rSNPs	diseases
10	nsv524682	chr1:144034888-144617179	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
11	esv1828275	chr1:144274482-145098718	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
12	nsv1014641	chr1:144337917-144880405	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
13	nsv998833	chr1:144337917-144885032	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
14	nsv1009682	chr1:144471974-144876884	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
15	nsv1008142	chr1:144471974-144880405	Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
16	nsv1001693	chr1:144471974-145290292	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	311 gene(s)	inside rSNPs	diseases
17	nsv831292	chr1:144506093-144613511	Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	248 gene(s)	inside rSNPs	diseases
18	nsv831303	chr1:144523643-144617215	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	248 gene(s)	inside rSNPs	diseases
19	nsv872206	chr1:144544101-144881389	Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv872207	chr1:144560355-144859086	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
21	nsv872208	chr1:144560355-144875799	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv946242	chr1:144588546-144622111	Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	esv1832561	chr1:144590080-144830258	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
24	esv1832493	chr1:144598061-144832598	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv872209	chr1:144600291-144881389	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
26	nsv946741	chr1:144606153-144612556	Weak transcription Strong transcription Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12086328	RP11-640M9.2	cis	Whole Blood	GTEx
rs12086328	RP11-640M9.2	cis	Nerve Tibial	GTEx
rs12086328	RP11-640M9.2	cis	Thyroid	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:144594600-144621200	Weak transcription	Gastric	stomach
2	chr1:144594600-144622000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:144594600-144622000	Weak transcription	Placenta	Placenta
4	chr1:144594800-144607600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:144594800-144608000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:144594800-144608000	Weak transcription	Fetal Brain Male	brain
7	chr1:144594800-144608600	Weak transcription	Psoas Muscle	Psoas
8	chr1:144594800-144609000	Weak transcription	A549	lung
9	chr1:144594800-144609000	Weak transcription	GM12878-XiMat	blood
10	chr1:144594800-144609200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:144594800-144618000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:144594800-144618000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:144594800-144618000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:144594800-144618000	Weak transcription	Adipose Nuclei	Adipose
15	chr1:144594800-144619400	Weak transcription	Aorta	Aorta
16	chr1:144594800-144620000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:144594800-144620200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:144594800-144620600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:144594800-144621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:144594800-144621200	Weak transcription	Fetal Lung	lung
21	chr1:144594800-144621200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:144594800-144621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:144594800-144621400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:144594800-144621600	Weak transcription	HSMM	muscle
25	chr1:144594800-144621800	Weak transcription	Brain Germinal Matrix	brain
26	chr1:144594800-144621800	Weak transcription	HSMMtube	muscle
27	chr1:144594800-144622000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:144594800-144622000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:144594800-144623400	Weak transcription	Primary T cells from cord blood	blood
30	chr1:144594800-144623400	Weak transcription	HUVEC	blood vessel
31	chr1:144594800-144624000	Weak transcription	Right Ventricle	heart
32	chr1:144595800-144623200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:144596200-144608800	Weak transcription	NHDF-Ad	bronchial
34	chr1:144596200-144612200	Weak transcription	NHEK	skin
35	chr1:144596200-144616600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:144596200-144618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:144596200-144621400	Weak transcription	Pancreas	Pancrea
38	chr1:144596400-144622000	Weak transcription	NH-A	brain
39	chr1:144598800-144621400	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:144598800-144623600	Weak transcription	Hela-S3	cervix
41	chr1:144599000-144608400	Weak transcription	Spleen	Spleen
42	chr1:144599000-144621200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:144599200-144621600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:144599400-144609000	Weak transcription	Fetal Brain Female	brain
45	chr1:144599400-144609600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:144599400-144618000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:144599400-144618000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:144599400-144618200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:144599400-144619400	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:144599400-144619400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links