Variant report

Variant	rs1553984
Chromosome Location	chr4:76554650-76554651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10009902	0.81[AMR][1000 genomes]
rs10014281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10025315	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10028884	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10029110	0.92[AMR][1000 genomes]
rs11097069	0.90[EUR][1000 genomes]
rs11097070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11729258	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11736474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737705	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13116639	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13118426	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13133699	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137468	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138717	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13140908	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464070	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464071	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546539	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548175	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553986	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1828629	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1967495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1967496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs226416	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2280095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292522	1.00[JPT][hapmap]
rs2869174	0.87[AMR][1000 genomes]
rs324682	0.87[AMR][1000 genomes]
rs324683	0.84[AMR][1000 genomes]
rs324685	0.92[AMR][1000 genomes]
rs324689	1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs324692	0.89[AMR][1000 genomes]
rs324695	1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs324707	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324708	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324711	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324715	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324716	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324717	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324718	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324721	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324724	0.89[AMR][1000 genomes]
rs324725	1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs324737	0.92[AMR][1000 genomes]
rs3796473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796485	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796488	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3853183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853184	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3942252	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4337757	0.86[EUR][1000 genomes]
rs4349625	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs436611	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs443952	1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs4859403	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859537	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4859542	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859544	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859545	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859546	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859547	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5020591	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6419115	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6531778	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531841	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6531866	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531867	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531868	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531889	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6531902	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6531903	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6826858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6828365	0.81[EUR][1000 genomes]
rs6829402	0.86[EUR][1000 genomes]
rs6832912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835702	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835819	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6842216	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6855321	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6858741	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72651313	0.83[AMR][1000 genomes]
rs7356270	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7356310	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7657871	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7659408	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7662940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7672378	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7674063	0.94[AMR][1000 genomes]
rs7674328	1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7677150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7685459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7691765	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7696241	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9942164	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76548200-76555200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:76548600-76555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:76553800-76555400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:76554000-76556600	Active TSS	Fetal Kidney	kidney
5	chr4:76554400-76555000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:76554400-76555000	Enhancers	Colon Smooth Muscle	Colon
7	chr4:76554400-76555200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:76554400-76555400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:76554400-76555400	Active TSS	Stomach Smooth Muscle	stomach
10	chr4:76554400-76556200	Active TSS	Brain Angular Gyrus	brain
11	chr4:76554400-76556200	Active TSS	Brain Hippocampus Middle	brain
12	chr4:76554400-76556200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr4:76554400-76556400	Active TSS	Brain Anterior Caudate	brain
14	chr4:76554400-76556600	Active TSS	Brain Cingulate Gyrus	brain
15	chr4:76554400-76556600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:76554400-76556800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:76554600-76554800	Flanking Active TSS	Fetal Brain Male	brain
18	chr4:76554600-76555000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr4:76554600-76555200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:76554600-76555200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:76554600-76555800	Active TSS	Brain Germinal Matrix	brain
22	chr4:76554600-76556000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:76554600-76556400	Active TSS	Brain Substantia Nigra	brain
24	chr4:76554600-76556600	Active TSS	A549	lung

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