Variant report

Variant	rs12062022
Chromosome Location	chr1:153729120-153729121
allele	C/T
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	POLR2A	chr1:153728932-153729221	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153699432..153703063-chr1:153728328..153730978,3	MCF-7	breast:
2	chr1:153720991..153724810-chr1:153725795..153729552,4	K562	blood:

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000238511	TF binding region
ENSG00000233222	TF binding region
ENSG00000143624	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000233222	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11264299	0.94[EUR][1000 genomes]
rs11264336	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1132619	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12068901	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070559	0.94[EUR][1000 genomes]
rs12071801	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076697	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097043	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097583	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34527123	1.00[ASN][1000 genomes]
rs36064263	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4073768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265191	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55658698	0.94[EUR][1000 genomes]
rs55778008	0.94[EUR][1000 genomes]
rs56167936	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56910871	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57314764	0.83[EUR][1000 genomes]
rs60100741	0.84[EUR][1000 genomes]
rs60316596	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60827720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803563	0.94[EUR][1000 genomes]
rs61803565	0.94[EUR][1000 genomes]
rs61803566	0.88[EUR][1000 genomes]
rs61803567	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61803571	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61803573	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61803652	1.00[ASN][1000 genomes]
rs6427085	0.90[EUR][1000 genomes]
rs6660232	0.84[EUR][1000 genomes]
rs6663011	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6663988	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6668229	0.83[EUR][1000 genomes]
rs6672371	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682411	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6687602	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6689176	0.94[EUR][1000 genomes]
rs74115713	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512561	0.84[EUR][1000 genomes]
rs7515716	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7520045	0.84[EUR][1000 genomes]
rs7520235	0.83[EUR][1000 genomes]
rs7556155	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556379	0.84[EUR][1000 genomes]
rs7556575	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12062022	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	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
4	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
7	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
8	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
12	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
14	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
20	chr1:153713000-153747000	Strong transcription	Dnd41	blood
21	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
25	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:153718800-153730000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:153719800-153731200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:153721000-153738200	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr1:153721800-153729600	Weak transcription	Psoas Muscle	Psoas
31	chr1:153722000-153735400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:153722000-153743800	Strong transcription	Fetal Stomach	stomach
33	chr1:153722200-153738000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:153722200-153742800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:153722400-153735200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:153722400-153735600	Strong transcription	Brain Hippocampus Middle	brain
37	chr1:153722400-153738200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:153722400-153743000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:153722400-153746200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:153722600-153742800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:153722600-153746600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:153722800-153732400	Strong transcription	Brain Angular Gyrus	brain
44	chr1:153722800-153738200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:153722800-153742800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:153723000-153729200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:153723000-153731000	Strong transcription	Brain Substantia Nigra	brain
48	chr1:153723000-153735400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:153723600-153735400	Strong transcription	Brain Anterior Caudate	brain
50	chr1:153723600-153735800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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