Variant report

Variant	rs817405
Chromosome Location	chr1:85619170-85619171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYDE2-1	chr1:85618178-85619886	NONHSAT004237

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11805576	1.00[AMR][1000 genomes]
rs17123230	1.00[AMR][1000 genomes]
rs17125247	1.00[AMR][1000 genomes]
rs2790912	1.00[AMR][1000 genomes]
rs709784	1.00[AMR][1000 genomes]
rs817402	1.00[AMR][1000 genomes]
rs817408	1.00[AMR][1000 genomes]
rs817412	1.00[AMR][1000 genomes]
rs817442	1.00[AMR][1000 genomes]
rs817443	1.00[AMR][1000 genomes]
rs817444	1.00[AMR][1000 genomes]
rs817448	1.00[AMR][1000 genomes]
rs817450	1.00[AMR][1000 genomes]
rs817454	1.00[AMR][1000 genomes]
rs817455	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs817459	1.00[AMR][1000 genomes]
rs817460	1.00[AMR][1000 genomes]
rs817461	1.00[AMR][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85603800-85632200	Weak transcription	Fetal Lung	lung
2	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
3	chr1:85608800-85629200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:85610600-85630600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:85611400-85629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:85615000-85621800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:85615400-85647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:85615400-85655200	Weak transcription	Lung	lung
10	chr1:85615600-85654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:85615800-85625200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:85615800-85627200	Weak transcription	Ovary	ovary
13	chr1:85615800-85627600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:85615800-85629400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:85615800-85630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:85615800-85632800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
18	chr1:85616000-85632200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:85616000-85634600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:85616000-85638800	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:85616400-85627600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:85616400-85635800	Weak transcription	Left Ventricle	heart
23	chr1:85617000-85619400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:85617400-85619200	Weak transcription	Fetal Intestine Large	intestine
25	chr1:85617800-85648000	Weak transcription	Liver	Liver
26	chr1:85618600-85619800	Enhancers	Fetal Heart	heart
27	chr1:85618800-85619200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:85618800-85619400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:85618800-85619800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:85618800-85619800	Flanking Active TSS	GM12878-XiMat	blood
31	chr1:85619000-85619200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:85619000-85619200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:85619000-85619200	Enhancers	Right Atrium	heart
34	chr1:85619000-85619400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:85619000-85629000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:85619000-85655000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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