Variant report

Variant	rs1890120
Chromosome Location	chr1:224026137-224026138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224023431..224026214-chr1:224032048..224035063,3	MCF-7	breast:
2	chr1:224007285..224009204-chr1:224024898..224026701,2	K562	blood:
3	chr1:224021776..224023617-chr1:224025728..224028035,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10915891	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10961	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs1153948	0.91[EUR][1000 genomes]
rs1415583	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2045733	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2126387	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856162	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57453172	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604731	0.84[YRI][hapmap]
rs6658516	0.87[EUR][1000 genomes]
rs6661430	0.88[EUR][1000 genomes]
rs6682353	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6699339	0.87[ASN][1000 genomes]
rs720757	0.94[ASN][1000 genomes]
rs7517814	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7543815	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7547098	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224010200-224026400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:224017600-224026800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224019000-224026400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:224019400-224026400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:224019400-224026400	Enhancers	Primary T cells from cord blood	blood
6	chr1:224019400-224027000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:224019600-224027400	Enhancers	Fetal Heart	heart
8	chr1:224019800-224026600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:224020200-224026400	Enhancers	HUVEC	blood vessel
10	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:224020800-224028600	Weak transcription	Placenta	Placenta
12	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:224021200-224027000	Enhancers	Brain Substantia Nigra	brain
14	chr1:224021400-224027000	Enhancers	Fetal Lung	lung
15	chr1:224021800-224026400	Enhancers	Stomach Mucosa	stomach
16	chr1:224022400-224026400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:224022400-224026600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:224022600-224026200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:224022800-224026400	Enhancers	NHLF	lung
20	chr1:224022800-224026800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:224023000-224026400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:224023000-224026800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:224023000-224027000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:224023000-224029000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:224023000-224030600	Weak transcription	Fetal Kidney	kidney
26	chr1:224023200-224026200	Enhancers	Liver	Liver
27	chr1:224023200-224026400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:224023200-224026400	Enhancers	Small Intestine	intestine
29	chr1:224023200-224026600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:224023200-224031600	Weak transcription	Hela-S3	cervix
31	chr1:224023400-224026400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr1:224023400-224026600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:224023400-224026600	Enhancers	Left Ventricle	heart
34	chr1:224023400-224026600	Enhancers	Dnd41	blood
35	chr1:224023400-224027000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:224023400-224027400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:224023600-224027000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:224023800-224026400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:224023800-224026600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:224023800-224026600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:224023800-224026600	Enhancers	Right Ventricle	heart
42	chr1:224023800-224027000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr1:224023800-224028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:224024000-224026200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:224024000-224026600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:224024000-224027800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:224024000-224028000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:224024000-224031800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:224024000-224031800	Weak transcription	Thymus	Thymus
50	chr1:224024200-224026400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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