Variant report

Variant	rs982447
Chromosome Location	chr7:106973534-106973535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1015411	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs10224503	0.81[AMR][1000 genomes]
rs10234355	0.94[CHB][hapmap]
rs11535285	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs12112877	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12667527	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12670688	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs12672451	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12673675	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs13230144	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17153981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17154040	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17154091	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs1858888	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2023685	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2107317	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237660	0.80[EUR][1000 genomes]
rs2237661	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2237665	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237668	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237671	0.80[AMR][1000 genomes]
rs2283038	0.90[CEU][hapmap]
rs2301801	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395868	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395869	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2520241	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520242	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520243	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2520245	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2520249	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520250	0.82[AMR][1000 genomes]
rs2520256	0.82[AMR][1000 genomes]
rs2712195	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2712196	0.80[AMR][1000 genomes]
rs2712201	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2712224	0.82[AMR][1000 genomes]
rs3094383	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34325395	0.82[AMR][1000 genomes]
rs3801964	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs3801966	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4727678	0.84[AMR][1000 genomes]
rs4727679	0.84[AMR][1000 genomes]
rs4727680	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs4727681	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4730235	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730237	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730238	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4730245	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs58391518	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62482493	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62482495	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482499	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62482502	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62482503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62482507	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482543	0.80[ASN][1000 genomes]
rs62483629	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483633	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62483634	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483640	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6949634	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7777950	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7785892	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7788271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788330	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790080	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803151	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9791733	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs986994	0.82[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs982447	BCAP29	Cis_1M	lymphoblastoid	RTeQTL
rs982447	COG5	cis	parietal	SCAN
rs982447	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106888800-106999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:106923800-106999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:106946200-106999800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:106946400-106978400	Weak transcription	Fetal Intestine Large	intestine
5	chr7:106946400-106983600	Weak transcription	Aorta	Aorta
6	chr7:106946400-106983600	Weak transcription	Fetal Intestine Small	intestine
7	chr7:106946400-106999400	Weak transcription	Pancreas	Pancrea
8	chr7:106952400-106973600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:106953800-106999400	Weak transcription	Left Ventricle	heart
10	chr7:106960000-106978200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:106960600-106974800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:106961200-106982400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:106963200-106974000	Weak transcription	K562	blood
14	chr7:106964200-106978400	Weak transcription	Liver	Liver
15	chr7:106964400-106977800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:106965400-106998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:106967600-106978400	Weak transcription	Fetal Stomach	stomach
18	chr7:106967600-106983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:106967800-106999800	Weak transcription	Fetal Heart	heart
20	chr7:106969200-106978200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:106969200-106984200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:106969800-106974200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:106973000-106973600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:106973000-106973600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr7:106973000-106973800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr7:106973000-106974000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:106973000-106974000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:106973000-106974200	Enhancers	HUVEC	blood vessel
29	chr7:106973000-106974400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr7:106973000-106974600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr7:106973200-106973600	Active TSS	Primary B cells from cord blood	blood
32	chr7:106973200-106973600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:106973200-106973600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr7:106973200-106973600	Weak transcription	Thymus	Thymus
35	chr7:106973200-106973800	Active TSS	GM12878-XiMat	blood
36	chr7:106973200-106974000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:106973200-106974600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr7:106973400-106973600	Enhancers	Dnd41	blood
39	chr7:106973400-106973600	Enhancers	NHDF-Ad	bronchial
40	chr7:106973400-106973600	Enhancers	NHEK	skin
41	chr7:106973400-106973800	Enhancers	Primary T cells from cord blood	blood
42	chr7:106973400-106973800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr7:106973400-106974000	Active TSS	Primary hematopoietic stem cells	blood
44	chr7:106973400-106974000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:106973400-106974000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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