Variant report

Variant	rs2888611
Chromosome Location	chr7:87103670-87103671
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1014283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10452935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10452936	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11974333	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11975741	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539936	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12539997	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1468615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1473152	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1473154	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1558375	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1558376	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17149637	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17149640	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17149641	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17149644	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17149647	0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap]
rs17149652	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17149660	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2071645	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2072383	0.82[MEX][hapmap]
rs2072384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2270187	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302385	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs2302386	0.84[JPT][hapmap]
rs2302387	1.00[ASW][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4148810	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4148811	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4148813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4148814	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs4148815	0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4148816	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4148817	0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4148818	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4148820	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4148824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4148826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45447097	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs45478299	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45479991	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45493392	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45496691	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45537841	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45546132	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs45553044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45560338	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45593435	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs45605032	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs45607141	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55747905	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60040620	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60123540	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60624924	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6971521	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6971745	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7782186	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7789645	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7793196	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1029486	chr7:86856387-87121976	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv539004	chr7:86856387-87121976	Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv1024376	chr7:86905796-87129346	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	esv3382480	chr7:87031452-87133648	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv464623	chr7:87040629-87139316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv607726	chr7:87040629-87139316	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv1792643	chr7:87069758-87108420	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv888684	chr7:87074964-87105795	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
18	nsv888689	chr7:87093247-87110017	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv888690	chr7:87093247-87122847	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2888611	FZD1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87094800-87103800	Weak transcription	Left Ventricle	heart
2	chr7:87095000-87104000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:87101600-87105200	Active TSS	Liver	Liver
4	chr7:87102400-87103800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:87102400-87104000	Flanking Active TSS	HepG2	liver
6	chr7:87102600-87103800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:87102600-87104000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr7:87102600-87104000	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:87102800-87103800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:87102800-87104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:87102800-87104000	Weak transcription	Psoas Muscle	Psoas
12	chr7:87103000-87104000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr7:87103000-87104000	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr7:87103200-87103800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:87103200-87104000	Enhancers	Colon Smooth Muscle	Colon
16	chr7:87103200-87104000	Enhancers	HSMMtube	muscle
17	chr7:87103400-87103800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr7:87103400-87103800	Enhancers	Primary hematopoietic stem cells	blood
19	chr7:87103400-87103800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:87103400-87103800	Enhancers	Adipose Nuclei	Adipose
21	chr7:87103400-87103800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
22	chr7:87103400-87104000	Weak transcription	Colonic Mucosa	Colon
23	chr7:87103400-87104000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr7:87103400-87104000	Enhancers	Osteobl	bone
25	chr7:87103400-87104200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:87103400-87104400	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr7:87103400-87104400	Active TSS	Stomach Smooth Muscle	stomach
28	chr7:87103400-87104600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr7:87103400-87104800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr7:87103400-87105000	Flanking Active TSS	GM12878-XiMat	blood
31	chr7:87103600-87103800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:87103600-87103800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr7:87103600-87103800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr7:87103600-87103800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
35	chr7:87103600-87103800	Enhancers	NH-A	brain
36	chr7:87103600-87104000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:87103600-87104800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:87103600-87104800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:87103600-87105200	Active TSS	Right Atrium	heart
40	chr7:87103600-87105400	Active TSS	Aorta	Aorta
41	chr7:87103600-87105400	Active TSS	Fetal Heart	heart
42	chr7:87103600-87105400	Active TSS	Right Ventricle	heart
43	chr7:87103600-87105600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr7:87103600-87105800	Active TSS	Rectal Smooth Muscle	rectum

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