Variant report

Variant	rs12025390
Chromosome Location	chr1:120216287-120216288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120214959..120216731-chr6:111195251..111197604,2	MCF-7	breast:
2	chr1:120204131..120206731-chr1:120214943..120217556,2	MCF-7	breast:
3	chr1:120215638..120218365-chr1:120219886..120221935,2	K562	blood:
4	chr1:120189265..120193710-chr1:120213010..120218911,11	MCF-7	breast:
5	chr1:120189180..120192171-chr1:120215646..120218336,2	K562	blood:
6	chr1:120215935..120218673-chr1:120225082..120226675,2	MCF-7	breast:
7	chr1:120171369..120174303-chr1:120214777..120217221,2	K562	blood:
8	chr1:120189291..120191976-chr1:120215677..120217877,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction
ENSG00000123505	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158797	1.00[JPT][hapmap]
rs10802131	1.00[JPT][hapmap]
rs10923884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923886	1.00[JPT][hapmap]
rs12023426	1.00[JPT][hapmap]
rs12030925	1.00[JPT][hapmap]
rs12042810	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12043284	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045485	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082229	1.00[JPT][hapmap]
rs12091329	0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs2843023	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS 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 target site	38 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	chr1:120203800-120217800	Weak transcription	Fetal Stomach	stomach
2	chr1:120210200-120218000	Weak transcription	GM12878-XiMat	blood
3	chr1:120212800-120218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:120214400-120216600	Enhancers	HUVEC	blood vessel
5	chr1:120214400-120216800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:120214600-120216600	Enhancers	NHEK	skin
7	chr1:120214800-120218000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:120215000-120216600	Enhancers	Osteobl	bone
9	chr1:120215000-120217800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:120215200-120216600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:120215200-120217400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:120215200-120217600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:120215200-120218000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:120215200-120219000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:120215200-120219600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:120215400-120217200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:120215400-120217800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:120215400-120217800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:120215400-120218000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:120215800-120216600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:120215800-120216600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:120215800-120216600	Enhancers	Hela-S3	cervix
23	chr1:120215800-120216800	Enhancers	Placenta	Placenta
24	chr1:120215800-120217400	Enhancers	Ovary	ovary
25	chr1:120215800-120218000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:120216000-120216600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:120216000-120216800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:120216000-120217000	Enhancers	HepG2	liver
29	chr1:120216000-120217000	Enhancers	NHLF	lung
30	chr1:120216000-120217200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:120216000-120217200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:120216000-120217200	Enhancers	Fetal Kidney	kidney
33	chr1:120216000-120217600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:120216000-120217600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:120216000-120217600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:120216000-120218000	Enhancers	HSMMtube	muscle
37	chr1:120216000-120218000	Enhancers	NH-A	brain
38	chr1:120216200-120216400	Enhancers	Fetal Intestine Small	intestine
39	chr1:120216200-120216600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:120216200-120216600	Enhancers	HMEC	breast
41	chr1:120216200-120217200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:120216200-120217400	Weak transcription	Stomach Mucosa	stomach
43	chr1:120216200-120217800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:120216200-120218000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:120216200-120218600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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