Variant report

Variant	rs774960
Chromosome Location	chr3:98848088-98848089
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1002155	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1016283	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1082505	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926320	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13097354	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1357676	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404096	0.80[ASN][1000 genomes]
rs1404103	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474354	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1520690	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520691	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1524217	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1524218	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1524219	0.84[EUR][1000 genomes]
rs1524221	0.82[EUR][1000 genomes]
rs1524222	0.82[EUR][1000 genomes]
rs1608594	0.84[ASN][1000 genomes]
rs1829934	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1851813	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1851818	0.80[EUR][1000 genomes]
rs1996976	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1996977	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2049278	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2091127	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2103121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2103122	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140278	0.80[ASN][1000 genomes]
rs2140280	0.80[ASN][1000 genomes]
rs2341713	0.84[EUR][1000 genomes]
rs2341714	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2681442	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682413	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682414	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682418	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2687686	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2687688	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2690239	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2690240	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2690241	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2690242	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2690243	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2690248	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2948597	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2948598	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2948599	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2948600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2948601	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2948602	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2948603	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2949161	0.84[EUR][1000 genomes]
rs2949167	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2966545	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2966547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2966548	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2966550	0.85[EUR][1000 genomes]
rs2966551	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2966552	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4271945	0.84[ASN][1000 genomes]
rs6778584	0.84[ASN][1000 genomes]
rs704587	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs704588	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704592	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141955	0.80[ASN][1000 genomes]
rs7617755	0.80[ASN][1000 genomes]
rs7652048	0.80[ASN][1000 genomes]
rs774732	0.83[EUR][1000 genomes]
rs774735	0.83[EUR][1000 genomes]
rs774736	0.82[EUR][1000 genomes]
rs774938	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs774944	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs774948	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs774949	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774950	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774956	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774957	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774959	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774961	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774964	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953629	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9839189	0.84[ASN][1000 genomes]
rs9847148	0.80[ASN][1000 genomes]
rs9852683	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877215	chr3:98804408-98884699	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv999649	chr3:98815244-98947271	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv536664	chr3:98815244-98947271	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1009629	chr3:98846458-98903887	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98834400-98848200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98844600-98851200	Enhancers	HSMM	muscle
3	chr3:98846800-98848400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:98846800-98849000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:98846800-98849000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:98846800-98849000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:98846800-98849000	Enhancers	HMEC	breast
8	chr3:98846800-98849400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:98847000-98848200	Enhancers	NHLF	lung
10	chr3:98847000-98848400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:98847000-98848800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:98847000-98848800	Enhancers	HUVEC	blood vessel
13	chr3:98847000-98849200	Enhancers	Osteobl	bone
14	chr3:98847000-98849400	Enhancers	NH-A	brain
15	chr3:98847000-98849400	Enhancers	NHDF-Ad	bronchial
16	chr3:98847200-98848200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:98847200-98848600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:98847200-98848800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:98847200-98848800	Enhancers	NHEK	skin
20	chr3:98847200-98849400	Enhancers	HSMMtube	muscle
21	chr3:98847600-98848400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:98847600-98848400	Enhancers	Brain Anterior Caudate	brain
23	chr3:98847600-98848400	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:98847800-98848400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:98848000-98848200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:98848000-98848200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:98848000-98848400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:98848000-98849000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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