Variant report

Variant	rs12070559
Chromosome Location	chr1:153743927-153743928
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	CTCF	chr1:153743664-153744950	SK-N-SH	brain:	n/a	chr1:153744561-153744577 chr1:153744555-153744576 chr1:153744560-153744578
2	CTCF	chr1:153743780-153743930	HBMEC	blood vessel:	n/a	n/a
3	CTCF	chr1:153743820-153743970	HPAF	blood vessel:	n/a	n/a
4	CTCF	chr1:153743780-153743930	BE2_C	brain:	n/a	n/a
5	POLR2A	chr1:153743822-153744028	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:153743836-153744064	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153734009..153737042-chr1:153743528..153745973,4	K562	blood:
2	chr1:153700596..153703068-chr1:153743594..153746100,2	MCF-7	breast:
3	chr1:153651116..153652910-chr1:153740976..153746594,4	MCF-7	breast:
4	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:

Variant related genes	Relation type
SLC27A3	TF binding region
ENSG00000143624	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000273026	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11264299	0.89[EUR][1000 genomes]
rs11264336	0.89[EUR][1000 genomes]
rs1132619	0.98[EUR][1000 genomes]
rs12062022	0.94[EUR][1000 genomes]
rs12068901	0.94[EUR][1000 genomes]
rs12070179	0.94[EUR][1000 genomes]
rs12071801	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12076697	0.89[EUR][1000 genomes]
rs12097043	0.94[EUR][1000 genomes]
rs12097583	0.94[EUR][1000 genomes]
rs36064263	0.98[EUR][1000 genomes]
rs4073768	0.94[EUR][1000 genomes]
rs41265191	0.94[EUR][1000 genomes]
rs55658698	0.89[EUR][1000 genomes]
rs55778008	0.89[EUR][1000 genomes]
rs56167936	0.98[EUR][1000 genomes]
rs56910871	0.89[EUR][1000 genomes]
rs60316596	0.92[EUR][1000 genomes]
rs60827720	0.94[EUR][1000 genomes]
rs61803563	0.89[EUR][1000 genomes]
rs61803565	0.89[EUR][1000 genomes]
rs61803566	0.87[EUR][1000 genomes]
rs61803567	0.92[EUR][1000 genomes]
rs61803571	0.85[EUR][1000 genomes]
rs61803573	0.94[EUR][1000 genomes]
rs6427085	0.85[EUR][1000 genomes]
rs6663011	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6663988	0.89[EUR][1000 genomes]
rs6672371	0.92[EUR][1000 genomes]
rs6682411	0.98[EUR][1000 genomes]
rs6687602	0.94[EUR][1000 genomes]
rs6689176	0.89[EUR][1000 genomes]
rs74115713	0.94[EUR][1000 genomes]
rs7515716	0.89[EUR][1000 genomes]
rs7556155	0.87[EUR][1000 genomes]
rs7556575	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12070559	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
3	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
7	chr1:153713000-153747000	Strong transcription	Dnd41	blood
8	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
11	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:153722400-153746200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:153722600-153746600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:153723600-153746800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:153725600-153747200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:153726400-153746200	Strong transcription	Fetal Lung	lung
19	chr1:153726800-153746000	Strong transcription	Ovary	ovary
20	chr1:153727800-153746400	Weak transcription	Fetal Heart	heart
21	chr1:153728400-153745800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:153730800-153747000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:153730800-153752600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:153731000-153747000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:153733400-153745400	Strong transcription	Osteobl	bone
26	chr1:153734800-153746000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:153735400-153747600	Weak transcription	K562	blood
28	chr1:153736400-153745400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:153736400-153745600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:153736600-153745400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:153736800-153746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:153737000-153744800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:153737200-153745200	Weak transcription	Right Atrium	heart
34	chr1:153737200-153746600	Strong transcription	Brain Anterior Caudate	brain
35	chr1:153739000-153746800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:153739200-153746000	Strong transcription	Aorta	Aorta
37	chr1:153739200-153746400	Strong transcription	Thymus	Thymus
38	chr1:153739400-153745800	Strong transcription	Colon Smooth Muscle	Colon
39	chr1:153739400-153746200	Strong transcription	Brain Hippocampus Middle	brain
40	chr1:153739400-153746400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr1:153739600-153744000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:153739600-153745600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:153739600-153746000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr1:153739600-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:153739600-153746800	Strong transcription	NHEK	skin
46	chr1:153739800-153745400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:153739800-153745600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:153739800-153745800	Strong transcription	Brain Substantia Nigra	brain
49	chr1:153739800-153746200	Strong transcription	Fetal Brain Female	brain
50	chr1:153739800-153746400	Strong transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links