Variant report

Variant	rs4700858
Chromosome Location	chr5:179497249-179497250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179490013..179492341-chr5:179495671..179497729,3	MCF-7	breast:
2	chr5:179494847..179497645-chr5:179497864..179501359,4	K562	blood:
3	chr5:179496103..179499035-chr5:179510851..179514542,4	K562	blood:
4	chr5:179467128..179469131-chr5:179495464..179498336,2	MCF-7	breast:
5	chr5:179452184..179453736-chr5:179495746..179497610,2	MCF-7	breast:
6	chr5:179332761..179336643-chr5:179497180..179500753,5	MCF-7	breast:
7	chr5:179332913..179335161-chr5:179495987..179497746,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253480	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10051632	0.96[ASN][1000 genomes]
rs10068529	0.82[CHB][hapmap]
rs10464097	0.87[AFR][1000 genomes]
rs11249666	0.88[AFR][1000 genomes]
rs13162328	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13176402	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1540526	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1947056	0.87[ASN][1000 genomes]
rs2083966	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs248316	0.80[TSI][hapmap]
rs27014	0.80[TSI][hapmap]
rs27016	0.82[TSI][hapmap]
rs27019	0.80[TSI][hapmap]
rs3749821	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235506	0.87[ASN][1000 genomes]
rs4290977	0.87[ASN][1000 genomes]
rs4340879	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs449511	0.82[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs4700859	0.94[AFR][1000 genomes]
rs4700862	0.83[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6601080	0.87[ASN][1000 genomes]
rs723889	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7706570	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7734329	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7734867	1.00[ASN][1000 genomes]
rs9329096	0.88[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4700858	RASGEF1C	cis	cerebellum	SCAN
rs4700858	RASGEF1C	cis	parietal	SCAN
rs4700858	CLTB	cis	parietal	SCAN
rs4700858	TRIM7	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179476000-179497800	Weak transcription	Lung	lung
2	chr5:179494800-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:179495000-179497800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr5:179495200-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:179495400-179499400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:179495600-179497600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:179495600-179497800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr5:179495600-179499200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:179495800-179499000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr5:179495800-179499200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:179496000-179497600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:179496200-179497400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr5:179496200-179498000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr5:179496200-179498000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr5:179496400-179497400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:179496400-179497600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:179496400-179497600	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr5:179496400-179497800	Enhancers	Small Intestine	intestine
19	chr5:179496400-179498400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr5:179496400-179498400	Bivalent/Poised TSS	GM12878-XiMat	blood
21	chr5:179496600-179497400	Enhancers	HMEC	breast
22	chr5:179496600-179497600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr5:179496600-179497600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:179496600-179497600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:179496600-179497600	Enhancers	Aorta	Aorta
26	chr5:179496600-179497600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr5:179496600-179497600	Flanking Active TSS	Fetal Lung	lung
28	chr5:179496600-179497800	Enhancers	Fetal Heart	heart
29	chr5:179496600-179497800	Flanking Active TSS	HepG2	liver
30	chr5:179496600-179498000	Flanking Active TSS	Fetal Kidney	kidney
31	chr5:179496600-179498200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:179496600-179498200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr5:179496600-179498400	Flanking Active TSS	K562	blood
34	chr5:179496600-179498400	Flanking Active TSS	NH-A	brain
35	chr5:179496600-179499200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:179496600-179499200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:179496600-179499400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:179496800-179497400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:179496800-179497400	Flanking Active TSS	Pancreas	Pancrea
40	chr5:179496800-179497400	Flanking Active TSS	Right Atrium	heart
41	chr5:179496800-179497600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:179496800-179497600	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr5:179496800-179497600	Flanking Active TSS	NHDF-Ad	bronchial
44	chr5:179496800-179497800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:179496800-179497800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:179496800-179497800	Flanking Active TSS	Liver	Liver
47	chr5:179496800-179497800	Flanking Active TSS	Fetal Stomach	stomach
48	chr5:179496800-179497800	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr5:179496800-179497800	Flanking Active TSS	Hela-S3	cervix
50	chr5:179496800-179498000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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