Variant report

Variant	rs10480747
Chromosome Location	chr7:120880573-120880574
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120879517..120881994-chr7:120882337..120885417,3	K562	blood:
2	chr7:120879517..120881082-chr7:120883141..120886021,2	K562	blood:
3	chr7:120873011..120874844-chr7:120878339..120881386,3	K562	blood:
4	chr7:120878568..120880747-chr7:120916933..120919501,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10225165	0.84[CEU][hapmap];0.93[ASN][1000 genomes]
rs10225276	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10266975	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10500083	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953932	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10953933	0.83[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10953934	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1106040	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11509199	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs11532789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763675	0.96[ASN][1000 genomes]
rs11765163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770502	0.96[ASN][1000 genomes]
rs11771945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533196	0.96[ASN][1000 genomes]
rs12539571	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12666947	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12671290	1.00[ASN][1000 genomes]
rs12672898	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12706333	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12706334	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317515	0.93[ASN][1000 genomes]
rs13244291	0.91[ASN][1000 genomes]
rs13247350	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13247392	0.91[ASN][1000 genomes]
rs1524506	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1524507	0.98[ASN][1000 genomes]
rs1534014	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs1534016	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534017	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1534018	0.98[ASN][1000 genomes]
rs1534019	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17284918	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17284988	0.97[ASN][1000 genomes]
rs17285023	0.81[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17357115	0.81[CEU][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1917119	0.98[ASN][1000 genomes]
rs1949803	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2140648	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2222543	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2272196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402563	0.85[CEU][hapmap];0.96[ASN][1000 genomes]
rs2536149	0.87[ASW][hapmap];0.83[LWK][hapmap]
rs3942607	1.00[ASN][1000 genomes]
rs4403351	0.96[ASN][1000 genomes]
rs4609139	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4731000	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4731001	1.00[ASN][1000 genomes]
rs4731002	0.96[ASN][1000 genomes]
rs4731003	0.91[ASN][1000 genomes]
rs4731005	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4731006	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731007	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4731008	0.93[ASN][1000 genomes]
rs4731009	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs60706788	0.96[ASN][1000 genomes]
rs6466773	1.00[ASN][1000 genomes]
rs6466774	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6942652	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6944914	0.96[ASN][1000 genomes]
rs6947934	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6948725	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6960849	0.96[ASN][1000 genomes]
rs6965195	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967129	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6970383	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs6977352	0.98[ASN][1000 genomes]
rs6978080	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6979948	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs71546706	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73217365	0.89[ASN][1000 genomes]
rs7778938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792071	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7795660	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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804720	0.91[ASN][1000 genomes]
rs7805374	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7806875	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7808120	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7810755	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7811248	0.96[ASN][1000 genomes]
rs798903	0.89[JPT][hapmap]
rs798907	0.89[JPT][hapmap]
rs798910	0.89[JPT][hapmap]
rs798914	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1031282	chr7:120667937-120887301	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv539099	chr7:120667937-120887301	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019025	chr7:120667937-120918696	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv539100	chr7:120667937-120918696	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv534342	chr7:120667938-120887300	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv428506	chr7:120719434-120891759	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv427802	chr7:120749159-120935856	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS 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 target site	19 gene(s)	inside rSNPs	diseases
12	nsv1015979	chr7:120836198-120881658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv539101	chr7:120836198-120881658	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases
16	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv889122	chr7:120860912-120906744	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2523024	chr7:120880522-120881925	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10480747	C7orf58	cis	cerebellum	SCAN
rs10480747	LMOD2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120844800-120881600	Weak transcription	HSMMtube	muscle
2	chr7:120863000-120884200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr7:120866400-120882600	Strong transcription	K562	blood
4	chr7:120868600-120887600	Weak transcription	Right Ventricle	heart
5	chr7:120872600-120936600	Weak transcription	Psoas Muscle	Psoas
6	chr7:120873400-120888800	Weak transcription	Fetal Heart	heart
7	chr7:120874800-120884200	Weak transcription	Fetal Stomach	stomach
8	chr7:120876000-120884200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:120876000-120884200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:120876000-120884200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:120876000-120889000	Weak transcription	Fetal Lung	lung
12	chr7:120876200-120884200	Weak transcription	Pancreas	Pancrea
13	chr7:120876200-120884400	Weak transcription	NHDF-Ad	bronchial
14	chr7:120876400-120884200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:120876600-120884600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:120877000-120887600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:120877200-120880800	Strong transcription	Liver	Liver
18	chr7:120877400-120880800	Strong transcription	Adipose Nuclei	Adipose
19	chr7:120877800-120884200	Weak transcription	Fetal Muscle Leg	muscle
20	chr7:120878000-120888600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:120878400-120884200	Weak transcription	Aorta	Aorta
22	chr7:120878400-120886200	Weak transcription	Fetal Kidney	kidney
23	chr7:120878600-120884000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:120878600-120884200	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:120878600-120884600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:120879200-120881600	Weak transcription	HSMM	muscle
27	chr7:120879200-120883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:120879200-120884200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:120879200-120884600	Weak transcription	Ovary	ovary
30	chr7:120879200-120884800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:120879200-120886200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:120879200-120887400	Weak transcription	NHLF	lung
33	chr7:120880200-120880600	Enhancers	Brain Germinal Matrix	brain
34	chr7:120880200-120887400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:120880400-120880600	Weak transcription	Left Ventricle	heart
36	chr7:120880400-120884200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links