Variant report

Variant	rs12026642
Chromosome Location	chr1:85615689-85615690
allele	C/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: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11161543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4907140	0.90[CEU][hapmap];0.84[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs61136219	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668323	0.81[AMR][1000 genomes]
rs7532784	0.96[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:45 , 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	chr1:85613800-85615800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:85613800-85615800	Enhancers	Osteobl	bone
13	chr1:85613800-85616000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:85613800-85616400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:85614000-85617600	Enhancers	Fetal Heart	heart
16	chr1:85614200-85615800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:85614200-85615800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:85614200-85615800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:85614200-85616000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:85614200-85616000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:85614200-85616000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:85614200-85616400	Enhancers	Left Ventricle	heart
23	chr1:85614400-85616000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:85614400-85618800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:85614800-85615800	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:85614800-85615800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:85614800-85616000	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:85614800-85619000	Weak transcription	Right Atrium	heart
29	chr1:85615000-85616000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:85615000-85616000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:85615000-85616000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:85615000-85616000	Enhancers	Right Ventricle	heart
33	chr1:85615000-85621800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:85615200-85615800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:85615200-85615800	Enhancers	Psoas Muscle	Psoas
36	chr1:85615400-85616000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:85615400-85647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:85615400-85655200	Weak transcription	Lung	lung
39	chr1:85615600-85615800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:85615600-85615800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:85615600-85615800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:85615600-85615800	Enhancers	Esophagus	oesophagus
43	chr1:85615600-85615800	Enhancers	Ovary	ovary
44	chr1:85615600-85616000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:85615600-85654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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