Variant report

Variant	rs3828541
Chromosome Location	chr4:100042262-100042263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10000357	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10009145	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015824	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020052	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1133483	0.87[AFR][1000 genomes]
rs1154402	0.81[AMR][1000 genomes]
rs1154404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1154415	1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11724783	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1311621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13121905	0.90[EUR][1000 genomes]
rs13127586	0.81[AMR][1000 genomes]
rs13148577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17595102	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes]
rs1800760	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893883	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2187483	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2602836	0.93[ASW][hapmap];0.86[YRI][hapmap]
rs2602844	0.87[AFR][1000 genomes]
rs2602852	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602861	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602871	0.85[EUR][1000 genomes]
rs2602874	0.90[AFR][1000 genomes]
rs2851264	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2851275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs28762430	0.84[EUR][1000 genomes]
rs28848249	0.90[EUR][1000 genomes]
rs34195655	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34511427	0.90[EUR][1000 genomes]
rs3857224	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4147544	1.00[JPT][hapmap]
rs4147545	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4147547	0.96[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs4148883	0.91[GIH][hapmap]
rs4148886	0.85[ASN][1000 genomes]
rs4577585	0.90[EUR][1000 genomes]
rs62325498	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6833176	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9307238	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9994326	0.88[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:100035000-100098200	Weak transcription	Ovary	ovary
4	chr4:100038800-100055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100040000-100043800	Weak transcription	Fetal Lung	lung
7	chr4:100040000-100045000	Weak transcription	Liver	Liver
8	chr4:100040000-100050800	Weak transcription	Fetal Intestine Large	intestine
9	chr4:100041000-100046400	Weak transcription	HepG2	liver
10	chr4:100041200-100042400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:100041200-100045000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:100041600-100042600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:100041600-100042600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:100041800-100042400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:100041800-100042400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:100042000-100042400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:100042000-100042600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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