Variant report

Variant	rs10953934
Chromosome Location	chr7:120901695-120901696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10225165	0.84[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10225276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10266975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10480747	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10500083	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10953932	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10953933	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1106040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11509199	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11532789	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11763675	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11765163	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11770502	0.82[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11771945	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12533196	0.97[ASN][1000 genomes]
rs12539571	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12666947	0.93[ASN][1000 genomes]
rs12671290	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12672898	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12706333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12706334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1317515	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13244291	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13247350	0.97[ASN][1000 genomes]
rs13247392	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1524506	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1524507	0.91[ASN][1000 genomes]
rs1534014	0.83[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1534016	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1534017	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1534018	0.91[ASN][1000 genomes]
rs1534019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17284918	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs17284988	0.90[ASN][1000 genomes]
rs17285023	1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs17357115	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1917119	0.91[ASN][1000 genomes]
rs1949803	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2140648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2222543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272196	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2402563	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3942607	0.93[ASN][1000 genomes]
rs4403351	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4609139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4731000	0.90[ASN][1000 genomes]
rs4731001	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4731002	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4731003	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4731005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731006	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4731007	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4731008	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4731009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60706788	0.97[ASN][1000 genomes]
rs6466773	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6466774	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6942652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6944914	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6947934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6948725	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6960849	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6965195	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6967129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6970383	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6977352	0.91[ASN][1000 genomes]
rs6978080	0.81[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs6979948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71546706	0.97[ASN][1000 genomes]
rs73217365	0.82[ASN][1000 genomes]
rs7778938	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7792071	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7795660	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7795692	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7804720	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7805374	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7806875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7808120	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7810755	0.97[ASN][1000 genomes]
rs7811248	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs798903	0.89[JPT][hapmap]
rs798907	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs798910	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs798914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10953934	C7orf58	cis	cerebellum	SCAN
rs10953934	LMOD2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120872600-120936600	Weak transcription	Psoas Muscle	Psoas
2	chr7:120886600-120910600	Weak transcription	Fetal Kidney	kidney
3	chr7:120887200-120906400	Weak transcription	HSMMtube	muscle
4	chr7:120888400-120906200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:120888400-120906400	Weak transcription	NHLF	lung
6	chr7:120888400-120910000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:120888600-120905600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:120888600-120905600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:120888600-120906400	Weak transcription	Aorta	Aorta
10	chr7:120888600-120907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:120888600-120907800	Weak transcription	Right Ventricle	heart
12	chr7:120888600-120908000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:120888600-120908200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:120888800-120937800	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:120889600-120902000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:120889600-120906200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:120889600-120906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:120889600-120913600	Weak transcription	NHDF-Ad	bronchial
19	chr7:120893400-120916600	Strong transcription	K562	blood
20	chr7:120893400-120916800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:120895800-120923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:120897600-120917200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:120898600-120904200	Strong transcription	Liver	Liver
24	chr7:120899400-120902000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:120899400-120907800	Weak transcription	Fetal Stomach	stomach
26	chr7:120900000-120902400	Strong transcription	Ovary	ovary
27	chr7:120900000-120918200	Weak transcription	Osteobl	bone
28	chr7:120901400-120903600	Strong transcription	Adipose Nuclei	Adipose
29	chr7:120901600-120902000	Strong transcription	HSMM	muscle
30	chr7:120901600-120902400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:120901600-120902400	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links