Variant report

Variant	rs7686428
Chromosome Location	chr4:100828161-100828162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10026048	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097676	0.95[JPT][hapmap]
rs11097677	0.95[JPT][hapmap]
rs11732776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935024	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935399	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11939538	0.84[ASW][hapmap];0.84[LWK][hapmap]
rs1365491	0.95[JPT][hapmap]
rs1365492	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1365495	0.91[JPT][hapmap]
rs17029563	0.95[JPT][hapmap]
rs17029583	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17029662	0.84[ASW][hapmap];0.84[LWK][hapmap]
rs1863608	0.90[JPT][hapmap]
rs1896166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961323	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1972698	0.95[JPT][hapmap]
rs2070738	0.89[CEU][hapmap]
rs2098937	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114442	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282588	0.91[JPT][hapmap]
rs2298735	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28404345	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866180	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28706589	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756087	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3775499	0.95[JPT][hapmap]
rs3775500	0.95[JPT][hapmap]
rs3775501	0.95[JPT][hapmap]
rs3775511	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4699764	0.86[JPT][hapmap]
rs4699765	0.90[JPT][hapmap]
rs60978748	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532833	0.95[JPT][hapmap]
rs6532835	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6532836	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811559	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6814895	0.95[JPT][hapmap]
rs6848337	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849599	0.83[ASW][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6854536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715239	0.91[JPT][hapmap]
rs7675947	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684872	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7689566	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692416	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919132	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs919133	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9307242	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7686428	MAPKSP1	cis	parietal	SCAN
rs7686428	MAPKSP1	cis	cerebellum	SCAN
rs7686428	NFKB1	cis	cerebellum	SCAN
rs7686428	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs7686428	DNAJB14	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100815600-100840000	Weak transcription	Small Intestine	intestine
2	chr4:100816000-100829600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:100816000-100839800	Weak transcription	Esophagus	oesophagus
4	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:100816000-100867000	Weak transcription	Lung	lung
6	chr4:100816200-100837600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:100816200-100838000	Weak transcription	Fetal Stomach	stomach
8	chr4:100816200-100838800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:100816200-100839800	Weak transcription	Aorta	Aorta
10	chr4:100816200-100840200	Weak transcription	Colonic Mucosa	Colon
11	chr4:100816200-100842200	Weak transcription	Pancreas	Pancrea
12	chr4:100816200-100851400	Weak transcription	A549	lung
13	chr4:100816200-100851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:100816200-100853600	Weak transcription	NHLF	lung
15	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:100816400-100828600	Weak transcription	HepG2	liver
17	chr4:100816400-100830600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:100816400-100837400	Weak transcription	Thymus	Thymus
19	chr4:100816400-100845800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:100816600-100837400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:100816600-100839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:100816600-100839800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:100816600-100841800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:100816600-100843800	Weak transcription	Right Ventricle	heart
25	chr4:100817800-100836400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:100818600-100831600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:100819000-100829600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:100819000-100831000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:100819000-100838600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:100819400-100829600	Strong transcription	HMEC	breast
31	chr4:100819600-100829800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:100819600-100839800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:100819800-100829800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:100820000-100830400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:100820000-100866200	Weak transcription	Fetal Heart	heart
36	chr4:100820600-100830400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:100820600-100834800	Strong transcription	Dnd41	blood
38	chr4:100820600-100838400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:100820800-100830000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:100820800-100830000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:100820800-100831400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:100821000-100829200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:100821000-100830600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:100821600-100830000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:100821600-100833600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr4:100821600-100833800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:100821800-100829200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:100821800-100829800	Strong transcription	Placenta	Placenta
49	chr4:100822000-100829200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:100822000-100829200	Strong transcription	Fetal Thymus	thymus

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