Variant report

Variant	rs12546965
Chromosome Location	chr8:1728292-1728293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:1726321..1728354-chr8:1771384..1774203,2	MCF-7	breast:
2	chr8:1716816..1721615-chr8:1726505..1732038,6	K562	blood:
3	chr8:1691178..1695166-chr8:1727484..1730315,3	MCF-7	breast:
4	chr8:1711245..1713893-chr8:1726417..1729246,3	K562	blood:
5	chr8:1681316..1685438-chr8:1724958..1729595,5	K562	blood:
6	chr8:1710542..1713448-chr8:1725280..1729246,5	K562	blood:
7	chr8:1727131..1730202-chr8:1731838..1734952,3	K562	blood:

Variant related genes	Relation type
ENSG00000253982	Chromatin interaction
ENSG00000182372	Chromatin interaction
ENSG00000104728	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11787218	1.00[CHB][hapmap]
rs3901161	1.00[CHB][hapmap]
rs41435746	1.00[CHB][hapmap]
rs55634012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742804	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55991725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56147268	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198692	0.85[EUR][1000 genomes]
rs56298638	0.83[EUR][1000 genomes]
rs6992443	1.00[CHB][hapmap]
rs7005428	1.00[CHB][hapmap]
rs7842741	1.00[CHB][hapmap]
rs9650491	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv889711	chr8:1591412-1904157	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv934075	chr8:1626857-1736355	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1034490	chr8:1654716-1782467	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv609527	chr8:1681733-1753497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	nsv870096	chr8:1682851-1767342	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
13	nsv465274	chr8:1685064-1728292	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv609528	chr8:1685064-1728292	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv532892	chr8:1687433-1839578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	esv2755149	chr8:1689290-1755281	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
17	nsv465275	chr8:1697086-1768004	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
18	nsv609529	chr8:1697086-1768004	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
19	nsv465276	chr8:1701432-1777571	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
20	nsv609530	chr8:1701432-1777571	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
21	nsv609531	chr8:1717036-1965389	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv932825	chr8:1719042-1736355	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12546965	CLN8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1713400-1735800	Weak transcription	Fetal Brain Male	brain
2	chr8:1713600-1729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:1714000-1729800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr8:1714400-1729200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:1715400-1729200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr8:1717400-1728400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:1717600-1731000	Weak transcription	Fetal Lung	lung
8	chr8:1718000-1732400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:1718000-1732800	Weak transcription	Fetal Heart	heart
10	chr8:1718000-1736000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:1718400-1733200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:1719800-1729200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr8:1721400-1733800	Weak transcription	Hela-S3	cervix
14	chr8:1721600-1732800	Weak transcription	Right Atrium	heart
15	chr8:1721600-1734200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:1721800-1729400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr8:1721800-1734000	Weak transcription	Colon Smooth Muscle	Colon
18	chr8:1722000-1730000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr8:1722000-1730200	Weak transcription	HUVEC	blood vessel
20	chr8:1722000-1730600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:1722000-1731000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr8:1722000-1734000	Weak transcription	Ovary	ovary
23	chr8:1722200-1734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:1722800-1734200	Weak transcription	Colonic Mucosa	Colon
25	chr8:1723200-1731200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:1724600-1728400	Weak transcription	HMEC	breast
27	chr8:1724800-1731200	Weak transcription	Brain Angular Gyrus	brain
28	chr8:1724800-1733200	Weak transcription	Brain Germinal Matrix	brain
29	chr8:1725000-1730400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:1725200-1728400	Weak transcription	Dnd41	blood
31	chr8:1725200-1728600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:1725200-1730600	Weak transcription	Fetal Brain Female	brain
33	chr8:1725200-1730800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr8:1725200-1731000	Weak transcription	Aorta	Aorta
35	chr8:1725400-1728400	Weak transcription	HepG2	liver
36	chr8:1725400-1730800	Weak transcription	Primary T cells from cord blood	blood
37	chr8:1725600-1728400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr8:1725600-1728400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr8:1725600-1728600	Weak transcription	Esophagus	oesophagus
40	chr8:1725600-1734000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr8:1725800-1729600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr8:1725800-1731000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:1726200-1728400	Enhancers	Fetal Thymus	thymus
44	chr8:1726200-1729200	Enhancers	Brain Hippocampus Middle	brain
45	chr8:1726200-1729800	Enhancers	Brain Cingulate Gyrus	brain
46	chr8:1726600-1728600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr8:1726600-1728600	Enhancers	A549	lung
48	chr8:1726600-1729200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr8:1726600-1729400	Enhancers	Brain Substantia Nigra	brain
50	chr8:1726800-1728400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links