Variant report

Variant	rs1689716
Chromosome Location	chr5:1876272-1876273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1797668..1799939-chr5:1875244..1876843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11133915	1.00[JPT][hapmap]
rs1684953	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684971	0.89[ASN][1000 genomes]
rs16901305	1.00[CHB][hapmap]
rs2232376	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv596893	chr5:1839498-1892759	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1018082	chr5:1849721-1884738	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv881470	chr5:1850563-1892759	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv881188	chr5:1852284-1892759	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1689716	LPCAT1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1873400-1876400	Bivalent Enhancer	Fetal Intestine Small	intestine
2	chr5:1874400-1877400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr5:1874600-1876400	Bivalent Enhancer	Fetal Stomach	stomach
4	chr5:1874600-1876600	Bivalent Enhancer	Fetal Brain Male	brain
5	chr5:1874600-1877200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr5:1874600-1877200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr5:1874800-1877400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:1875000-1876400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:1875000-1876600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr5:1875000-1876600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:1875000-1876600	Enhancers	Pancreas	Pancrea
12	chr5:1875000-1877200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:1875200-1877400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:1875400-1876400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:1875400-1876400	Bivalent Enhancer	Fetal Intestine Large	intestine
16	chr5:1875400-1876600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:1875400-1876600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
18	chr5:1875400-1876800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:1875400-1876800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
20	chr5:1875400-1877200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr5:1875400-1877200	Enhancers	Fetal Heart	heart
22	chr5:1875600-1876400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr5:1875600-1876400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr5:1875600-1876400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
25	chr5:1875600-1876400	Bivalent Enhancer	Brain Germinal Matrix	brain
26	chr5:1875600-1877000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:1875600-1877000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:1875600-1877200	Weak transcription	HMEC	breast
29	chr5:1875800-1876400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:1875800-1876400	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr5:1875800-1876400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
32	chr5:1875800-1876400	Bivalent Enhancer	Psoas Muscle	Psoas
33	chr5:1875800-1876400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
34	chr5:1875800-1876600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
35	chr5:1875800-1876600	Enhancers	Liver	Liver
36	chr5:1875800-1876600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
37	chr5:1875800-1876600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
38	chr5:1875800-1876800	Bivalent Enhancer	Fetal Brain Female	brain
39	chr5:1875800-1877400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:1876000-1876400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
41	chr5:1876000-1876400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr5:1876000-1876400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
43	chr5:1876000-1876400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
44	chr5:1876000-1876400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:1876000-1876400	Bivalent Enhancer	Fetal Lung	lung
46	chr5:1876000-1876600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:1876000-1876600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr5:1876000-1876600	Flanking Active TSS	Right Ventricle	heart
49	chr5:1876000-1877200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:1876200-1876400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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