Variant report

Variant	rs3789335
Chromosome Location	chr20:14319889-14319890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12329405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs204629	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs204636	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs204637	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs204645	0.81[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2145560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2208454	0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2208456	0.84[JPT][hapmap]
rs2327846	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6033952	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs6042695	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs6105236	0.92[JPT][hapmap]
rs6105243	0.84[JPT][hapmap]
rs6105245	0.91[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105246	0.85[JPT][hapmap]
rs6105247	0.84[JPT][hapmap]
rs6105250	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110220	0.92[JPT][hapmap]
rs6110235	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6110241	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6110242	0.91[CEU][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6110247	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6110251	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6110252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6110255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6110259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6110263	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6110264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135108	0.87[EUR][1000 genomes]
rs6135109	0.84[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs6135124	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6135125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6135127	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8126410	0.91[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv432101	chr20:14294196-14353346	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1799128	chr20:14309952-14324140	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine
2	chr20:14318400-14320600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:14318400-14320600	Weak transcription	Fetal Heart	heart
4	chr20:14318400-14321200	Weak transcription	Fetal Intestine Small	intestine
5	chr20:14318400-14321800	Weak transcription	Fetal Intestine Large	intestine
6	chr20:14318400-14322200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:14318400-14322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:14318400-14322400	Weak transcription	Adipose Nuclei	Adipose
9	chr20:14318400-14322400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:14318400-14322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:14318400-14322600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:14318400-14322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr20:14318400-14322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:14318400-14322600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr20:14318400-14322600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:14318400-14322600	Weak transcription	Psoas Muscle	Psoas
17	chr20:14318400-14322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr20:14318400-14322600	Weak transcription	Stomach Mucosa	stomach
19	chr20:14318400-14323400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr20:14318400-14325400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:14318400-14325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:14318600-14322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:14318800-14320600	Weak transcription	A549	lung
24	chr20:14318800-14323400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr20:14319600-14320400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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