Variant report

Variant	rs4693780
Chromosome Location	chr4:87641219-87641220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10008165	0.91[GIH][hapmap]
rs10016074	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10019950	0.92[ASN][1000 genomes]
rs10023787	0.87[GIH][hapmap]
rs10029671	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs1021101	0.95[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs1026861	0.87[GIH][hapmap]
rs1035191	0.84[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs10516778	0.94[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097115	0.82[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs11561681	0.82[AMR][1000 genomes]
rs11930396	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs11947018	0.83[GIH][hapmap]
rs12331502	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12503659	0.91[ASN][1000 genomes]
rs12510802	0.88[ASN][1000 genomes]
rs13113689	0.84[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1420621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1481833	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs17012072	0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs17419295	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs17419627	0.80[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs17419929	0.82[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs17420607	0.94[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17420966	0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17453839	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs17454154	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17454662	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17694112	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs2006842	0.84[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs2054592	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054593	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.92[ASN][1000 genomes]
rs2230600	0.94[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2287147	0.82[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs3775236	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3775238	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775239	0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs4263359	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4693150	0.80[AMR][1000 genomes]
rs4693152	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4693784	0.82[AMR][1000 genomes]
rs55670248	0.82[AMR][1000 genomes]
rs57954319	0.87[ASN][1000 genomes]
rs6531932	0.87[GIH][hapmap]
rs67867077	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665791	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72665795	0.80[AMR][1000 genomes]
rs7688019	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs9307020	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs9307026	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs969734	0.94[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9993042	0.87[GIH][hapmap];0.80[JPT][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4693780	LIN54	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
6	chr4:87593800-87641400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:87594400-87642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:87594400-87659800	Weak transcription	Ovary	ovary
9	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
10	chr4:87623400-87643000	Weak transcription	Fetal Lung	lung
11	chr4:87625200-87651600	Weak transcription	Esophagus	oesophagus
12	chr4:87625400-87643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:87628800-87641600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:87628800-87641800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
16	chr4:87635200-87641800	Weak transcription	NHLF	lung
17	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
18	chr4:87635400-87648200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:87635600-87651600	Weak transcription	Lung	lung
20	chr4:87636400-87644600	Weak transcription	Fetal Intestine Small	intestine
21	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:87636800-87643400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:87637200-87661200	Weak transcription	Pancreas	Pancrea
24	chr4:87638200-87641600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:87638600-87643600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:87638600-87644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:87639000-87643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:87639200-87641600	Weak transcription	Osteobl	bone
29	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
30	chr4:87639400-87641800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:87639400-87739200	Weak transcription	A549	lung
32	chr4:87639600-87641400	Weak transcription	NHDF-Ad	bronchial
33	chr4:87639600-87643200	Weak transcription	Fetal Kidney	kidney
34	chr4:87639600-87644400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:87639600-87644400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:87639800-87643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:87640200-87643200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:87640200-87652000	Weak transcription	HMEC	breast
39	chr4:87640400-87641400	Weak transcription	NHEK	skin
40	chr4:87640400-87643000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:87640400-87643000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:87640600-87641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:87640600-87641800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:87640600-87643200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:87640800-87641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:87641000-87641600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:87641000-87641600	Enhancers	Brain Anterior Caudate	brain
48	chr4:87641000-87642000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:87641000-87642600	Enhancers	Brain Hippocampus Middle	brain
50	chr4:87641000-87642800	Enhancers	Brain Substantia Nigra	brain

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