Variant report

Variant	rs3796804
Chromosome Location	chr4:82009707-82009708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10002442	0.87[EUR][1000 genomes]
rs10857207	0.86[JPT][hapmap]
rs1112880	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1112881	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1113771	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11723025	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11723204	0.86[JPT][hapmap]
rs11724815	0.83[EUR][1000 genomes]
rs11731129	0.82[JPT][hapmap]
rs13125120	0.85[EUR][1000 genomes]
rs13130117	0.87[EUR][1000 genomes]
rs1443538	0.82[JPT][hapmap]
rs1443539	0.86[JPT][hapmap]
rs1443540	0.89[JPT][hapmap]
rs1443545	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs17005046	0.87[EUR][1000 genomes]
rs17005047	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17005059	0.86[JPT][hapmap]
rs17005060	0.86[JPT][hapmap]
rs17005062	0.82[JPT][hapmap]
rs17005063	0.81[JPT][hapmap]
rs2028645	0.82[JPT][hapmap]
rs2289682	0.82[JPT][hapmap]
rs28454856	0.89[EUR][1000 genomes]
rs2868131	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2868132	0.85[JPT][hapmap]
rs2868133	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2868134	1.00[CEU][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2868139	0.86[JPT][hapmap]
rs28685252	0.85[EUR][1000 genomes]
rs2903748	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34281791	0.89[EUR][1000 genomes]
rs34954944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35176186	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3822224	0.90[JPT][hapmap]
rs4565072	0.89[EUR][1000 genomes]
rs6821258	0.86[JPT][hapmap]
rs6833113	0.87[EUR][1000 genomes]
rs7671128	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7675843	0.82[JPT][hapmap]
rs7679480	0.88[CEU][hapmap]
rs7695150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7700247	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs980767	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829984	chr4:81979988-82113977	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 susceptibility	22174851	GWAS catalog

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:81998200-82030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:82004000-82017200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:82005800-82019000	Weak transcription	Fetal Intestine Large	intestine
4	chr4:82006200-82024800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:82006600-82014400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:82006800-82012000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:82006800-82024800	Weak transcription	NHDF-Ad	bronchial
8	chr4:82007600-82010400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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