Variant report

Variant	rs8006539
Chromosome Location	chr14:71189754-71189755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71189704..71191620-chr14:71192243..71194827,2	MCF-7	breast:
2	chr14:71189656..71192635-chr14:71218301..71220303,2	MCF-7	breast:
3	chr14:71189314..71191908-chr14:71220289..71222021,3	MCF-7	breast:
4	chr14:71188747..71190799-chr14:71193873..71196833,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED6-3	chr14:71189244-71193302	NONHSAT037576

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10129529	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10134929	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10139774	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11158880	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11620710	0.83[CHB][hapmap]
rs11851046	0.88[ASN][1000 genomes]
rs12433469	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs12883244	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs2332457	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs3829955	0.80[MEX][hapmap]
rs4902847	0.81[CHB][hapmap]
rs4902848	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs6573976	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144832	0.84[ASN][1000 genomes]
rs7151405	0.83[CHB][hapmap]
rs7151957	0.91[ASN][1000 genomes]
rs7154907	0.83[CHB][hapmap]
rs7160912	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs8005459	0.83[CHB][hapmap]
rs886600	0.83[CHB][hapmap];0.88[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71177200-71195600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:71178600-71189800	Weak transcription	Fetal Brain Female	brain
3	chr14:71179800-71193200	Weak transcription	Right Atrium	heart
4	chr14:71180600-71193800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:71180600-71196800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:71180600-71196800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:71180800-71193600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:71180800-71196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:71180800-71200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr14:71181200-71195800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:71183200-71190200	Enhancers	Fetal Intestine Small	intestine
12	chr14:71183200-71192200	Enhancers	Fetal Intestine Large	intestine
13	chr14:71184400-71194400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:71185400-71198800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:71185800-71196400	Weak transcription	Colonic Mucosa	Colon
16	chr14:71185800-71196600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr14:71185800-71198600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
19	chr14:71186000-71190000	Weak transcription	Placenta	Placenta
20	chr14:71186000-71190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:71186000-71190600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr14:71186000-71195400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:71186000-71195600	Weak transcription	Pancreas	Pancrea
24	chr14:71186000-71196600	Weak transcription	Gastric	stomach
25	chr14:71186000-71196600	Weak transcription	Lung	lung
26	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
28	chr14:71186200-71190000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:71186600-71189800	Weak transcription	Esophagus	oesophagus
30	chr14:71187400-71190000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr14:71188000-71190200	Enhancers	HepG2	liver
32	chr14:71188000-71196800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr14:71188400-71189800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:71188400-71190400	Enhancers	A549	lung
35	chr14:71188600-71190600	Weak transcription	NHEK	skin
36	chr14:71188600-71193200	Weak transcription	Adipose Nuclei	Adipose
37	chr14:71188600-71195600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr14:71188600-71198600	Weak transcription	Liver	Liver
39	chr14:71188800-71189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:71188800-71190800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:71188800-71191200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr14:71188800-71192800	Weak transcription	Psoas Muscle	Psoas
43	chr14:71188800-71193400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:71188800-71194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr14:71188800-71198400	Strong transcription	HMEC	breast
46	chr14:71189600-71190400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr14:71189600-71193800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr14:71189600-71196000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr14:71189600-71196000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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