Variant report

Variant	rs1866755
Chromosome Location	chr4:74978340-74978341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr4:74978325-74978646	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr4:74977768-74978605	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr4:74977195-74978407	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr4:74977564-74978709	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr4:74978107-74978652	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74976407..74978358-chr4:74989024..74991226,2	K562	blood:
2	chr4:74969971..74972171-chr4:74976711..74978462,2	K562	blood:

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10938107	0.87[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs11725704	0.81[EUR][1000 genomes]
rs11733208	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12642974	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs13124617	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13128896	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371794	0.81[EUR][1000 genomes]
rs1371798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837559	0.87[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs3806792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4121652	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491641	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs518867	0.81[EUR][1000 genomes]
rs546829	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs549280	0.94[EUR][1000 genomes]
rs72652928	0.80[EUR][1000 genomes]
rs72652934	0.93[EUR][1000 genomes]
rs7667376	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684973	0.86[JPT][hapmap]
rs7686861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs882638	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9131	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981458	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3379316	chr4:74977405-74978942	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1866755	G3BP2	cis	parietal	SCAN
rs1866755	UTP3	cis	parietal	SCAN
rs1866755	CXCL6	cis	parietal	SCAN
rs1866755	CCNG2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74972000-74982000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:74972800-74980200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:74973000-74978600	Enhancers	HUVEC	blood vessel
4	chr4:74973400-74980200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:74974200-74981000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr4:74975600-74980000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:74975600-74980800	Enhancers	NHDF-Ad	bronchial
8	chr4:74975800-74978600	Enhancers	HSMMtube	muscle
9	chr4:74975800-74980000	Enhancers	HMEC	breast
10	chr4:74975800-74980800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:74975800-74980800	Enhancers	Osteobl	bone
12	chr4:74975800-74981800	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:74975800-74982600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:74976000-74980200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:74976000-74982200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:74976000-74982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:74976000-74984400	Enhancers	Hela-S3	cervix
18	chr4:74976200-74979000	Enhancers	NH-A	brain
19	chr4:74976600-74978400	Enhancers	A549	lung
20	chr4:74976600-74978600	Enhancers	HSMM	muscle
21	chr4:74976600-74978800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:74976600-74979200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:74976600-74979600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:74976600-74980800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:74977000-74978400	Enhancers	Adipose Nuclei	Adipose
26	chr4:74977000-74978400	Enhancers	Left Ventricle	heart
27	chr4:74977000-74978400	Enhancers	Stomach Mucosa	stomach
28	chr4:74977000-74980800	Enhancers	Placenta	Placenta
29	chr4:74977200-74981000	Weak transcription	Liver	Liver
30	chr4:74977200-74982200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:74977200-74983000	Weak transcription	Fetal Intestine Large	intestine
32	chr4:74977400-74978400	Enhancers	Esophagus	oesophagus
33	chr4:74977400-74978400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:74977400-74978400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:74977400-74978400	Flanking Active TSS	NHEK	skin
36	chr4:74977400-74978600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr4:74977400-74980600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:74977400-74982400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:74977600-74978400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:74977600-74978400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:74977600-74978400	Enhancers	Right Atrium	heart
42	chr4:74977600-74978600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:74977800-74978400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr4:74977800-74978400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:74977800-74978400	Enhancers	Brain Anterior Caudate	brain
46	chr4:74977800-74978600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:74977800-74979000	Enhancers	NHLF	lung
48	chr4:74978000-74978400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr4:74978000-74978400	Enhancers	Aorta	Aorta
50	chr4:74978000-74978400	Enhancers	Brain Cingulate Gyrus	brain

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