Variant report

Variant	rs6042678
Chromosome Location	chr20:14319186-14319187
allele	C/T
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:43)

rs_ID	r²[population]
rs1114952	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1114953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1555411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994496	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16994499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[ASN][1000 genomes]
rs16994501	1.00[CHB][hapmap]
rs1998487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2181530	0.87[ASN][1000 genomes]
rs2208457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327820	1.00[ASN][1000 genomes]
rs2876375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs35253731	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4813154	0.87[ASN][1000 genomes]
rs4814292	1.00[ASN][1000 genomes]
rs55763358	1.00[ASN][1000 genomes]
rs55985306	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033905	1.00[ASN][1000 genomes]
rs6033907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs6033916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033917	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033946	1.00[CHB][hapmap]
rs6033952	0.83[YRI][hapmap]
rs6042596	0.87[ASN][1000 genomes]
rs6042601	1.00[ASN][1000 genomes]
rs6042606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs6042614	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042616	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6042677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042679	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6042695	0.82[YRI][hapmap]
rs6074706	1.00[ASN][1000 genomes]
rs6074707	1.00[ASN][1000 genomes]
rs6079359	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6079360	1.00[ASN][1000 genomes]
rs6079371	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73901234	0.82[ASN][1000 genomes]
rs8120919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912190	1.00[ASN][1000 genomes]
rs9967919	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[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	chr20:14318400-14319600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:14318400-14320600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:14318400-14320600	Weak transcription	Fetal Heart	heart
5	chr20:14318400-14321200	Weak transcription	Fetal Intestine Small	intestine
6	chr20:14318400-14321800	Weak transcription	Fetal Intestine Large	intestine
7	chr20:14318400-14322200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr20:14318400-14322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:14318400-14322400	Weak transcription	Adipose Nuclei	Adipose
10	chr20:14318400-14322400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr20:14318400-14322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:14318400-14322600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:14318400-14322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr20:14318400-14322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:14318400-14322600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:14318400-14322600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr20:14318400-14322600	Weak transcription	Psoas Muscle	Psoas
18	chr20:14318400-14322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr20:14318400-14322600	Weak transcription	Stomach Mucosa	stomach
20	chr20:14318400-14323400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr20:14318400-14325400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:14318400-14325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr20:14318600-14322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:14318800-14320600	Weak transcription	A549	lung
25	chr20:14318800-14323400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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