Variant report

Variant	rs817401
Chromosome Location	chr1:85615880-85615881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85615173..85616173-chr16:187955..188702,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000103148	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1674162	0.93[EUR][1000 genomes]
rs1674175	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17382610	0.80[TSI][hapmap]
rs17386490	0.87[EUR][1000 genomes]
rs4907025	0.91[EUR][1000 genomes]
rs61769452	0.87[EUR][1000 genomes]
rs61769454	0.85[EUR][1000 genomes]
rs817389	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817390	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817392	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817394	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817398	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817403	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs817404	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs817411	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817415	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817422	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817423	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817425	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817428	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817434	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817436	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817438	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817445	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817446	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs817447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs817451	1.00[EUR][1000 genomes]
rs817453	1.00[EUR][1000 genomes]
rs817456	0.93[EUR][1000 genomes]
rs817457	0.83[EUR][1000 genomes]
rs860140	0.93[EUR][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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85603800-85618800	Weak transcription	Gastric	stomach
2	chr1:85603800-85632200	Weak transcription	Fetal Lung	lung
3	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
4	chr1:85608800-85629200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:85610600-85630600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85611400-85617000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:85611400-85629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:85612800-85616000	Enhancers	GM12878-XiMat	blood
10	chr1:85613600-85616000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:85613800-85616000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr1:85613800-85616400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:85614000-85617600	Enhancers	Fetal Heart	heart
14	chr1:85614200-85616000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:85614200-85616000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:85614200-85616000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:85614200-85616400	Enhancers	Left Ventricle	heart
18	chr1:85614400-85616000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:85614400-85618800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:85614800-85616000	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:85614800-85619000	Weak transcription	Right Atrium	heart
22	chr1:85615000-85616000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:85615000-85616000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:85615000-85616000	Enhancers	Colon Smooth Muscle	Colon
25	chr1:85615000-85616000	Enhancers	Right Ventricle	heart
26	chr1:85615000-85621800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:85615400-85616000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:85615400-85647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:85615400-85655200	Weak transcription	Lung	lung
30	chr1:85615600-85616000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:85615600-85654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:85615800-85617000	Weak transcription	Psoas Muscle	Psoas
33	chr1:85615800-85617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:85615800-85625200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:85615800-85627200	Weak transcription	Ovary	ovary
36	chr1:85615800-85627600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:85615800-85629400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:85615800-85630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:85615800-85632800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus

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