Variant report

Variant	rs3791186
Chromosome Location	chr1:153934303-153934304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:153934241-153934841	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:153934269-153934410	Hela-S3	cervix:	n/a	n/a
3	MAX	chr1:153934293-153934829	GM12878	blood:	n/a	n/a
4	MTA3	chr1:153933944-153934520	GM12878	blood:	n/a	n/a
5	WRNIP1	chr1:153933881-153934941	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:153934046-153937128	GM12891	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153933595..153935263-chr1:154149711..154151786,2	MCF-7	breast:
2	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:
3	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
4	chr1:153885199..153886799-chr1:153933054..153934567,2	MCF-7	breast:
5	chr1:153747107..153752136-chr1:153929206..153936862,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000273026	TF binding region
CRTC2	TF binding region
ENSG00000189171	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10127484	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10494303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908512	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908525	0.86[EUR][1000 genomes]
rs10908526	0.86[EUR][1000 genomes]
rs11264573	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11264621	0.85[EUR][1000 genomes]
rs11264736	0.84[EUR][1000 genomes]
rs12142733	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2252508	0.88[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2841102	0.83[JPT][hapmap]
rs6661009	0.84[EUR][1000 genomes]
rs6671362	0.81[EUR][1000 genomes]
rs7414227	0.81[CEU][hapmap]
rs7522030	0.81[CEU][hapmap]
rs7549032	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription 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 miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3791186	CREB3L4	cis	Artery Tibial	GTEx
rs3791186	SLC27A3	cis	cerebellum	SCAN
rs3791186	HAX1	cis	cerebellum	SCAN
rs3791186	FLG	cis	parietal	SCAN
rs3791186	PSMD4	cis	parietal	SCAN
rs3791186	CREB3L4	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153931000-153935800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:153931400-153934400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:153931600-153934400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:153931600-153934400	Weak transcription	HSMM	muscle
5	chr1:153931600-153934600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:153931600-153934600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:153931600-153934600	Genic enhancers	Fetal Muscle Leg	muscle
8	chr1:153931600-153934600	Enhancers	Psoas Muscle	Psoas
9	chr1:153931800-153934400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:153932000-153934400	Weak transcription	Fetal Brain Male	brain
11	chr1:153932000-153934600	Genic enhancers	Gastric	stomach
12	chr1:153932400-153934600	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr1:153932800-153934400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:153932800-153934400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:153932800-153935000	Genic enhancers	Spleen	Spleen
16	chr1:153933000-153934600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:153933000-153934600	Genic enhancers	Brain Germinal Matrix	brain
18	chr1:153933200-153934400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:153933200-153934600	Weak transcription	Ovary	ovary
20	chr1:153933400-153934400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:153933400-153934400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:153933400-153934400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:153933400-153934400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:153933400-153934600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:153933400-153934600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:153933400-153934600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:153933400-153935000	Weak transcription	Aorta	Aorta
28	chr1:153933800-153934400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
29	chr1:153933800-153934400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr1:153933800-153934400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:153933800-153934400	Enhancers	Brain Hippocampus Middle	brain
32	chr1:153933800-153934400	Genic enhancers	Fetal Lung	lung
33	chr1:153933800-153934400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
34	chr1:153933800-153934600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:153933800-153934600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
36	chr1:153933800-153934600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
37	chr1:153933800-153934600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:153933800-153934600	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:153933800-153934600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:153933800-153934600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:153933800-153934600	Transcr. at gene 5' and 3'	Placenta	Placenta
42	chr1:153933800-153934800	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
43	chr1:153933800-153934800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
44	chr1:153933800-153934800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr1:153933800-153934800	Enhancers	Fetal Heart	heart
46	chr1:153933800-153934800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr1:153933800-153935000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:153934000-153934400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:153934000-153934400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:153934000-153934400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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