Variant report

Variant	rs6885346
Chromosome Location	chr5:42499923-42499924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11949415	1.00[AMR][1000 genomes]
rs11954925	1.00[AMR][1000 genomes]
rs1509459	1.00[AMR][1000 genomes]
rs16872562	1.00[AMR][1000 genomes]
rs16872586	1.00[AMR][1000 genomes]
rs4346776	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871782	1.00[AMR][1000 genomes]
rs6878694	1.00[AMR][1000 genomes]
rs7702407	1.00[AMR][1000 genomes]
rs7702961	1.00[AMR][1000 genomes]
rs7709329	1.00[AMR][1000 genomes]
rs7718944	1.00[AMR][1000 genomes]
rs7726811	1.00[AMR][1000 genomes]
rs7730534	1.00[AMR][1000 genomes]
rs7731927	1.00[AMR][1000 genomes]
rs7737776	1.00[AMR][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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42495200-42500000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:42496000-42501200	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr5:42496400-42500200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:42496600-42500000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:42496600-42502200	Enhancers	Liver	Liver
6	chr5:42496800-42500000	Weak transcription	NHEK	skin
7	chr5:42496800-42503200	Weak transcription	HMEC	breast
8	chr5:42498600-42500800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr5:42498600-42507600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:42498600-42514800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:42499000-42501000	Enhancers	Adipose Nuclei	Adipose
12	chr5:42499200-42500400	Enhancers	Esophagus	oesophagus
13	chr5:42499200-42500400	Enhancers	Gastric	stomach
14	chr5:42499200-42500400	Enhancers	Pancreas	Pancrea
15	chr5:42499200-42500400	Enhancers	Psoas Muscle	Psoas
16	chr5:42499200-42500400	Enhancers	Right Atrium	heart
17	chr5:42499200-42500600	Enhancers	Fetal Muscle Leg	muscle
18	chr5:42499200-42500600	Enhancers	Right Ventricle	heart
19	chr5:42499200-42501000	Enhancers	Ovary	ovary
20	chr5:42499200-42503400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:42499400-42500400	Enhancers	Fetal Stomach	stomach
22	chr5:42499400-42500800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:42499400-42500800	Enhancers	Fetal Heart	heart
24	chr5:42499400-42501000	Enhancers	Colon Smooth Muscle	Colon
25	chr5:42499400-42501000	Enhancers	Rectal Smooth Muscle	rectum
26	chr5:42499600-42500000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:42499800-42500400	Enhancers	Left Ventricle	heart
28	chr5:42499800-42500600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:42499800-42500600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:42499800-42500600	Enhancers	Stomach Smooth Muscle	stomach
31	chr5:42499800-42500800	Enhancers	Fetal Lung	lung

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