Variant report

Variant	rs12068901
Chromosome Location	chr1:153742469-153742470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153742464-153742688	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153707400..153709904-chr1:153740195..153742998,2	MCF-7	breast:
2	chr1:153740321..153742761-chr1:153949643..153951682,2	MCF-7	breast:
3	chr1:153739733..153741257-chr1:153741754..153743438,2	K562	blood:
4	chr1:153651116..153652910-chr1:153740976..153746594,4	MCF-7	breast:
5	chr1:153538611..153540631-chr1:153741714..153743429,2	K562	blood:
6	chr1:153698143..153700265-chr1:153739778..153743356,3	MCF-7	breast:

No data

Variant related genes	Relation type
SLC27A3	TF binding region
ENSG00000143543	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000272654	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs11264299	0.94[EUR][1000 genomes]
rs11264336	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1132619	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12062022	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070179	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070559	0.94[EUR][1000 genomes]
rs12071801	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076697	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097043	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34527123	1.00[ASN][1000 genomes]
rs36064263	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4073768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265191	0.93[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	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56910871	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57314764	0.83[EUR][1000 genomes]
rs60100741	0.84[EUR][1000 genomes]
rs60316596	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60827720	0.99[AFR][1000 genomes];1.00[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	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61803567	0.98[EUR][1000 genomes]
rs61803571	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61803573	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61803652	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6427085	0.90[EUR][1000 genomes]
rs6660232	0.84[EUR][1000 genomes]
rs6663011	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6663988	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6668229	0.83[EUR][1000 genomes]
rs6672371	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682411	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6687602	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6689176	0.94[EUR][1000 genomes]
rs74115713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512561	0.84[EUR][1000 genomes]
rs7515716	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7520045	0.84[EUR][1000 genomes]
rs7520235	0.83[EUR][1000 genomes]
rs7556155	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556379	0.84[EUR][1000 genomes]
rs7556575	0.93[AMR][1000 genomes];0.98[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12068901	INTS3	cis	inferior olivary nucleus	BrainEAC
rs12068901	INTS3	cis	brain	BrainEAC
rs12068901	INTS3	cis	temporal cortex	BrainEAC
rs12068901	INTS3	cis	substantia nigra	BrainEAC
rs12068901	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL
rs12068901	INTS3	cis	cerebellar cortex	BrainEAC
rs12068901	INTS3	cis	hippocampus	BrainEAC
rs12068901	INTS3	cis	occipital cortex	BrainEAC
rs12068901	INTS3	cis	frontal cortex	BrainEAC
rs12068901	INTS3	cis	intralobular white matter	BrainEAC
rs12068901	INTS3	cis	thalamus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
5	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
9	chr1:153713000-153747000	Strong transcription	Dnd41	blood
10	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
13	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:153722000-153743800	Strong transcription	Fetal Stomach	stomach
16	chr1:153722200-153742800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:153722400-153743000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:153722400-153746200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:153722600-153742800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:153722600-153746600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:153722800-153742800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:153723600-153746800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:153725600-153747200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:153726400-153746200	Strong transcription	Fetal Lung	lung
26	chr1:153726800-153746000	Strong transcription	Ovary	ovary
27	chr1:153727800-153746400	Weak transcription	Fetal Heart	heart
28	chr1:153728400-153745800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:153729400-153743200	Strong transcription	HSMM	muscle
30	chr1:153730800-153747000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:153730800-153752600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:153731000-153747000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:153733200-153742800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:153733400-153745400	Strong transcription	Osteobl	bone
35	chr1:153734000-153743000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:153734800-153746000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:153735400-153747600	Weak transcription	K562	blood
38	chr1:153736400-153745400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:153736400-153745600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:153736600-153742800	Strong transcription	Left Ventricle	heart
41	chr1:153736600-153743800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:153736600-153745400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:153736800-153743800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:153736800-153746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:153737000-153744800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153737200-153745200	Weak transcription	Right Atrium	heart
47	chr1:153737200-153746600	Strong transcription	Brain Anterior Caudate	brain
48	chr1:153738600-153742600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:153738800-153743000	Genic enhancers	Fetal Intestine Small	intestine
50	chr1:153739000-153746800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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