Variant report

Variant	rs4700855
Chromosome Location	chr5:179487258-179487259
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179484896..179487600-chr5:179495650..179498856,3	K562	blood:
2	chr5:179480070..179481635-chr5:179485420..179487501,2	K562	blood:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10061480	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10068529	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10068594	0.82[ASN][1000 genomes]
rs10078977	0.81[CHB][hapmap]
rs10903246	0.88[CHD][hapmap]
rs12153541	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12653944	0.86[CHD][hapmap]
rs12656219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193718	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs1961583	0.84[ASN][1000 genomes]
rs2009728	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2083968	0.81[AMR][1000 genomes]
rs2120631	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2278661	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2386701	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2386704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248316	0.88[CHD][hapmap]
rs248319	0.80[JPT][hapmap]
rs27014	0.88[CHD][hapmap]
rs27016	0.88[CHD][hapmap]
rs27017	0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs3828698	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4130025	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4466125	0.83[ASN][1000 genomes]
rs449511	0.88[CHD][hapmap]
rs4700860	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62405020	0.83[ASN][1000 genomes]
rs62405021	0.83[ASN][1000 genomes]
rs6884290	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7728341	0.85[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs857181	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap]
rs9329096	0.83[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4700855	RASGEF1C	cis	cerebellum	SCAN
rs4700855	RASGEF1C	cis	parietal	SCAN
rs4700855	CLTB	cis	parietal	SCAN
rs4700855	BTNL9	cis	cerebellum	SCAN
rs4700855	MAML1	cis	cerebellum	SCAN
rs4700855	LTC4S	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
3	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
4	chr5:179476000-179497800	Weak transcription	Lung	lung
5	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
6	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:179477400-179495000	Weak transcription	Gastric	stomach
8	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
9	chr5:179478800-179493800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
11	chr5:179480400-179488200	Weak transcription	Fetal Brain Male	brain
12	chr5:179480600-179494000	Weak transcription	Fetal Lung	lung
13	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:179481600-179494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:179482000-179490200	Weak transcription	HepG2	liver
17	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:179484200-179488200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:179484200-179489800	Weak transcription	NHEK	skin
21	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179484400-179490000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:179484400-179495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:179484800-179487600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr5:179484800-179494000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:179485000-179489000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr5:179485000-179493200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:179485200-179488600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:179485600-179489800	Weak transcription	Fetal Brain Female	brain
30	chr5:179485800-179488600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr5:179485800-179489000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:179485800-179489000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr5:179486000-179487800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:179486000-179488600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:179486000-179488800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr5:179486000-179488800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:179486000-179489200	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:179486000-179489800	Enhancers	Brain Substantia Nigra	brain
39	chr5:179486200-179488200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:179486200-179488400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr5:179486200-179488400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:179486200-179489000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:179486400-179488400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr5:179486400-179489200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr5:179486600-179487400	Enhancers	Brain Angular Gyrus	brain
46	chr5:179486600-179488600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:179486600-179488800	Enhancers	Brain Hippocampus Middle	brain
48	chr5:179486600-179494000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:179486800-179487400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:179486800-179487800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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