Variant report

Variant	rs11976018
Chromosome Location	chr7:99122437-99122438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99122361..99125551-chr7:99169280..99172960,3	K562	blood:
2	chr7:99122366..99125169-chr7:99126048..99128824,3	K562	blood:
3	chr7:99122266..99124155-chr7:99149460..99151190,2	MCF-7	breast:
4	chr7:99100876..99102774-chr7:99122043..99124875,2	MCF-7	breast:
5	chr7:99102510..99104412-chr7:99119717..99122482,2	K562	blood:

Variant related genes	Relation type
ENSG00000221909	Chromatin interaction
ENSG00000196652	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011024	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs10225314	0.87[JPT][hapmap]
rs10238965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs10244158	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253937	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap]
rs10265385	0.81[ASN][1000 genomes]
rs10270459	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap]
rs10271049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10271582	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10272998	0.82[ASW][hapmap];0.92[CEU][hapmap];0.92[MKK][hapmap]
rs10279308	0.84[CEU][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11978089	0.84[CEU][hapmap]
rs13227795	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13437771	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs2240384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240385	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280600	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.81[EUR][1000 genomes]
rs2687086	0.84[JPT][hapmap]
rs2740561	0.81[JPT][hapmap]
rs28457808	0.84[ASN][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34777615	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800960	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801288	0.92[CEU][hapmap];0.89[MKK][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901286	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45540134	0.82[ASN][1000 genomes]
rs4646450	0.82[ASW][hapmap];0.85[CEU][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap];0.81[MKK][hapmap]
rs58222677	0.81[ASN][1000 genomes]
rs60301933	0.84[ASN][1000 genomes]
rs61159815	0.82[ASN][1000 genomes]
rs61402640	0.86[ASN][1000 genomes]
rs61543997	0.86[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap];0.81[MKK][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6962772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794682	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7804551	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs883403	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs940336	0.86[CHB][hapmap];0.89[JPT][hapmap]

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	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11976018	CYP3A5	cis	parietal	SCAN
rs11976018	CPSF4	cis	parietal	SCAN
rs11976018	GATS	cis	parietal	SCAN
rs11976018	ACTL6B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99103800-99125600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99104200-99123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:99105000-99126000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:99105000-99126400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:99105000-99128000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:99105000-99128000	Weak transcription	Fetal Heart	heart
7	chr7:99105000-99128800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:99105000-99129400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:99105400-99125400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:99105400-99126200	Weak transcription	Stomach Mucosa	stomach
11	chr7:99105600-99124400	Weak transcription	Psoas Muscle	Psoas
12	chr7:99107000-99126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:99107400-99126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:99107600-99126000	Strong transcription	Fetal Stomach	stomach
15	chr7:99108400-99126000	Strong transcription	Fetal Thymus	thymus
16	chr7:99108600-99125200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:99108600-99126200	Strong transcription	Dnd41	blood
18	chr7:99111800-99123400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:99112200-99123600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:99112400-99127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:99113200-99127800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:99113600-99125600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:99114400-99123000	Weak transcription	Colonic Mucosa	Colon
24	chr7:99114600-99123000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:99114600-99123000	Weak transcription	Small Intestine	intestine
26	chr7:99114600-99123000	Weak transcription	NHEK	skin
27	chr7:99114600-99123200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:99114600-99123200	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:99114600-99123400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:99114600-99123600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:99114600-99123600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:99114600-99123600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:99114600-99123600	Weak transcription	Pancreas	Pancrea
34	chr7:99114600-99123800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:99114800-99123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:99114800-99126400	Weak transcription	Fetal Brain Male	brain
37	chr7:99115200-99123200	Weak transcription	Brain Angular Gyrus	brain
38	chr7:99115800-99123400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:99116200-99123400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:99116800-99126200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:99117000-99125400	Strong transcription	Liver	Liver
42	chr7:99117000-99125600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:99117000-99126000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr7:99117000-99126200	Strong transcription	HSMMtube	muscle
45	chr7:99117200-99125800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:99117800-99123000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:99117800-99123000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:99117800-99123200	Weak transcription	Fetal Lung	lung
49	chr7:99117800-99123200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:99117800-99123200	Weak transcription	HepG2	liver

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