Variant report

Variant	rs1706823
Chromosome Location	chr15:45479351-45479352
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45465361..45468029-chr15:45478692..45480743,2	MCF-7	breast:
2	chr15:45457736..45460170-chr15:45478587..45480947,2	MCF-7	breast:
3	chr15:45457275..45460718-chr15:45477484..45481344,4	K562	blood:
4	chr15:45457610..45461525-chr15:45477333..45480560,5	MCF-7	breast:
5	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
6	chr15:45458222..45460718-chr15:45477355..45481212,4	K562	blood:
7	chr15:45461602..45463661-chr15:45476012..45479858,4	K562	blood:
8	chr15:45477456..45480320-chr15:45491100..45493481,2	MCF-7	breast:
9	chr15:45474753..45476915-chr15:45477928..45479578,2	MCF-7	breast:
10	chr15:45471595..45473672-chr15:45478332..45480462,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260035	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10450971	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12440127	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12898733	0.89[ASN][1000 genomes]
rs1611896	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1617207	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1625404	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1625779	0.93[ASN][1000 genomes]
rs1628717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1632144	0.93[ASN][1000 genomes]
rs1648280	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1648284	0.89[ASN][1000 genomes]
rs1648288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648290	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs1648291	0.85[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648292	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1648296	0.89[ASN][1000 genomes]
rs1648298	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1648299	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648300	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648301	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648314	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs1648315	0.92[ASN][1000 genomes]
rs1706765	0.94[JPT][hapmap]
rs1706779	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1706819	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs1706828	0.92[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1706833	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1706836	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2277611	1.00[TSI][hapmap]
rs2292468	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2413777	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2458238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458240	1.00[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2458241	0.92[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2467839	0.89[ASN][1000 genomes]
rs2668738	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2668750	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899376	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs2899377	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4775824	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58701250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7167481	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs732622	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938129	1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs938130	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	esv3339591	chr15:45478685-45481233	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
9	esv3450392	chr15:45479060-45481133	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45473200-45480400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:45475800-45479400	Flanking Active TSS	Fetal Brain Female	brain
3	chr15:45476000-45480200	Weak transcription	K562	blood
4	chr15:45476800-45479400	Flanking Active TSS	HepG2	liver
5	chr15:45477200-45479600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:45477200-45480400	Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr15:45477400-45479400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr15:45477400-45479800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:45477800-45479400	Flanking Active TSS	HSMM	muscle
10	chr15:45477800-45479600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:45477800-45479800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:45478000-45479400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:45478000-45479400	Flanking Active TSS	Colon Smooth Muscle	Colon
14	chr15:45478000-45479400	Flanking Active TSS	HSMMtube	muscle
15	chr15:45478000-45479600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr15:45478000-45479600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:45478000-45480200	Enhancers	Placenta	Placenta
18	chr15:45478200-45479400	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr15:45478200-45479600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr15:45478200-45479800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr15:45478200-45480600	Active TSS	Fetal Kidney	kidney
22	chr15:45478400-45479400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:45478600-45479400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr15:45478600-45479400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:45478600-45479400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:45478600-45479400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:45478600-45479400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:45478600-45479400	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr15:45478600-45479400	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr15:45478600-45479400	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr15:45478600-45479400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr15:45478600-45479400	Flanking Active TSS	Fetal Brain Male	brain
33	chr15:45478600-45479400	Flanking Active TSS	Fetal Stomach	stomach
34	chr15:45478600-45479600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr15:45478600-45479600	Flanking Active TSS	Liver	Liver
36	chr15:45478600-45479600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:45478600-45479600	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr15:45478600-45479800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:45478600-45479800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr15:45478800-45479400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr15:45478800-45479400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:45478800-45479400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr15:45478800-45479400	Bivalent Enhancer	Fetal Thymus	thymus
44	chr15:45478800-45479400	Enhancers	Pancreas	Pancrea
45	chr15:45478800-45479400	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr15:45478800-45479400	Flanking Active TSS	Right Atrium	heart
47	chr15:45478800-45479400	Flanking Active TSS	Right Ventricle	heart
48	chr15:45478800-45479400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr15:45478800-45479400	Enhancers	Stomach Mucosa	stomach
50	chr15:45478800-45479600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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