Variant report

Variant	rs56167936
Chromosome Location	chr1:153746610-153746611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153745735-153749410	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:153746322-153746668	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153746588-153746638	NB4	blood:	n/a
2	chr1:153746588-153746638	HAEpiC	amniotic membrane:	n/a
3	chr1:153746588-153746638	HEK293	kidney:	embryo
4	chr1:153746588-153746638	Jurkat	blood:	n/a
5	chr1:153746588-153746638	U87	brain:	n/a
6	chr1:153746588-153746638	AoSMC	blood vessel:	n/a
7	chr1:153746588-153746638	BE2_C	brain:	n/a
8	chr1:153746588-153746638	K562	blood:	n/a
9	chr1:153746588-153746638	Hela-S3	cervix:	n/a
10	chr1:153746588-153746638	AG10803	skin:	n/a
11	chr1:153746588-153746638	PANC-1	pancreas:	n/a
12	chr1:153746588-153746638	SKMC	muscle:	n/a
13	chr1:153746588-153746638	HCPEpiC	choroid plexus:	n/a
14	chr1:153746588-153746638	GM12892	blood:	n/a
15	chr1:153746588-153746638	GM06990	blood:	n/a
16	chr1:153746588-153746638	NHDF-neo	bronchial:	n/a
17	chr1:153746588-153746638	SK-N-SH	brain:	n/a
18	chr1:153746588-153746638	AG09309	skin:	n/a
19	chr1:153746588-153746638	HCF	heart:	n/a
20	chr1:153746588-153746638	GM12878	blood:	n/a
21	chr1:153746588-153746638	Caco-2	colon:	n/a
22	chr1:153746588-153746638	SK-N-MC	brain:	n/a
23	chr1:153746588-153746638	HPAEpiC	pulmonary alveolar:	n/a
24	chr1:153746588-153746638	CMK	blood:	n/a
25	chr1:153746588-153746638	MCF-7	breast:	n/a
26	chr1:153746588-153746638	NH-A	brain:	n/a
27	chr1:153746588-153746638	HRCEpiC	kidney:	n/a
28	chr1:153746588-153746638	HRPEpiC	eye:	n/a
29	chr1:153746588-153746638	GM19239	blood:	n/a
30	chr1:153746588-153746638	HCT-116	colon:	n/a
31	chr1:153746588-153746638	A549	lung:	n/a
32	chr1:153746588-153746638	NT2-D1	testis:	n/a
33	chr1:153746588-153746638	NHBE	bronchial:	n/a
34	chr1:153746588-153746638	PrEC	prostate:	n/a
35	chr1:153746588-153746638	IMR90	lung:	fetal
36	chr1:153746588-153746638	HUVEC	blood vessel:	n/a
37	chr1:153746588-153746638	HNPCEpiC	eye:	n/a
38	chr1:153746588-153746638	HMEC	breast:	n/a
39	chr1:153746588-153746638	SK-N-SH_RA	brain:	n/a
40	chr1:153746588-153746638	AG04450	lung:	fetal
41	chr1:153746588-153746638	ProgFib	skin:	n/a
42	chr1:153746588-153746638	ovcar-3	ovarian:	n/a
43	chr1:153746588-153746638	Hepatocyte	liver:	n/a
44	chr1:153746588-153746638	RPTEC	kidney:	n/a
45	chr1:153746588-153746638	HEEpiC	esophagus:	n/a
46	chr1:153746588-153746638	LNCaP	prostate:	n/a
47	chr1:153746588-153746638	GM12891	blood:	n/a
48	chr1:153746588-153746638	MCF10A-Er-Src	breast:	n/a
49	chr1:153746588-153746638	HepG2	liver:	n/a
50	chr1:153746588-153746638	HRE	kidney:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153679034..153681144-chr1:153743976..153746673,2	MCF-7	breast:
2	chr1:153745383..153747706-chr1:153962241..153964631,3	K562	blood:
3	chr1:153537152..153539160-chr1:153746062..153748854,2	MCF-7	breast:
4	chr1:153745179..153749280-chr1:153961747..153968478,7	MCF-7	breast:
5	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
6	chr1:153652004..153654217-chr1:153745758..153747753,2	K562	blood:
7	chr1:153720924..153726415-chr1:153745287..153750957,9	MCF-7	breast:

No data

Variant related genes	Relation type
SLC27A3	TF binding region
SLC27A3	CpG island
ENSG00000169418	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000231416	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000233222	Chromatin interaction
ENSG00000273026	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11264299	0.90[EUR][1000 genomes]
rs11264336	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1132619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062022	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12068901	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12070179	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12070559	0.98[EUR][1000 genomes]
rs12071801	0.98[EUR][1000 genomes]
rs12076697	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12097043	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12097583	0.96[EUR][1000 genomes]
rs36064263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073768	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41265191	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55658698	0.90[EUR][1000 genomes]
rs55778008	0.90[EUR][1000 genomes]
rs56910871	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60100741	0.81[EUR][1000 genomes]
rs60316596	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60827720	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61803563	0.90[EUR][1000 genomes]
rs61803565	0.90[EUR][1000 genomes]
rs61803566	0.85[EUR][1000 genomes]
rs61803567	0.94[EUR][1000 genomes]
rs61803571	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61803573	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427085	0.87[EUR][1000 genomes]
rs6660232	0.81[EUR][1000 genomes]
rs6663011	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663988	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6672371	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682411	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687602	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6689176	0.90[EUR][1000 genomes]
rs74115713	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7512561	0.81[EUR][1000 genomes]
rs7515716	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7520045	0.81[EUR][1000 genomes]
rs7556155	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7556379	0.81[EUR][1000 genomes]
rs7556575	0.96[AMR][1000 genomes];0.94[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
rs56167936	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	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:153713000-153747000	Strong transcription	Dnd41	blood
3	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:153723600-153746800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:153725600-153747200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:153730800-153747000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:153730800-153752600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:153731000-153747000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:153735400-153747600	Weak transcription	K562	blood
12	chr1:153739000-153746800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:153739600-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:153739600-153746800	Strong transcription	NHEK	skin
15	chr1:153740400-153746800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:153740400-153747200	Weak transcription	Psoas Muscle	Psoas
17	chr1:153740800-153747000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:153740800-153747400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:153740800-153747800	Weak transcription	Small Intestine	intestine
20	chr1:153741000-153747200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:153741400-153747200	Genic enhancers	Fetal Muscle Leg	muscle
22	chr1:153741400-153747400	Genic enhancers	Placenta	Placenta
23	chr1:153741800-153747200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:153741800-153747400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:153742000-153746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:153742200-153746800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:153742400-153747400	Weak transcription	Fetal Brain Male	brain
28	chr1:153742600-153747400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:153742600-153747600	Enhancers	HUVEC	blood vessel
30	chr1:153742800-153747600	Weak transcription	NH-A	brain
31	chr1:153743000-153746800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:153743000-153747200	Strong transcription	Fetal Intestine Small	intestine
33	chr1:153743200-153747800	Weak transcription	HSMM	muscle
34	chr1:153743400-153746800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr1:153743400-153747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:153743400-153747200	Weak transcription	NHDF-Ad	bronchial
37	chr1:153744000-153747000	Strong transcription	NHLF	lung
38	chr1:153744400-153746800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:153744400-153747000	Strong transcription	Brain Angular Gyrus	brain
40	chr1:153744400-153747200	Genic enhancers	Fetal Stomach	stomach
41	chr1:153744600-153746800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:153744600-153747800	Weak transcription	HSMMtube	muscle
43	chr1:153745000-153747800	Weak transcription	A549	lung
44	chr1:153745200-153746800	Weak transcription	Stomach Mucosa	stomach
45	chr1:153745200-153747000	Weak transcription	HMEC	breast
46	chr1:153745200-153747400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:153745200-153747400	Enhancers	Right Atrium	heart
48	chr1:153745200-153748000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr1:153745400-153747200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:153745400-153747200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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