Variant report

Variant	rs1648290
Chromosome Location	chr15:45464768-45464769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45457064..45458836-chr15:45462821..45464924,2	MCF-7	breast:
2	chr15:45458639..45462602-chr15:45463163..45466877,10	K562	blood:
3	chr15:45461861..45465831-chr15:45472049..45473955,3	K562	blood:
4	chr15:45464381..45467214-chr15:45569783..45571800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259520	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10450971	0.86[ASN][1000 genomes]
rs12440127	0.86[ASN][1000 genomes]
rs12898733	0.84[ASN][1000 genomes]
rs1611896	0.94[ASN][1000 genomes]
rs1617207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1625404	0.97[ASN][1000 genomes]
rs1625779	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628717	0.91[ASN][1000 genomes]
rs1632144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648280	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1648284	0.84[ASN][1000 genomes]
rs1648288	0.91[ASN][1000 genomes]
rs1648291	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs1648292	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1648296	0.84[ASN][1000 genomes]
rs1648298	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs1648299	0.91[ASN][1000 genomes]
rs1648300	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs1648301	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs1648314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648315	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1706765	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1706779	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1706819	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706823	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]
rs1706828	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs1706833	0.88[ASN][1000 genomes]
rs1706836	0.88[ASN][1000 genomes]
rs2277611	1.00[TSI][hapmap]
rs2292468	0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2413777	0.86[ASN][1000 genomes]
rs2458238	0.92[ASN][1000 genomes]
rs2458240	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs2458241	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs2467839	0.84[ASN][1000 genomes]
rs2668738	0.85[ASN][1000 genomes]
rs2668750	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2899376	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs2899377	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4775824	0.86[ASN][1000 genomes]
rs58701250	0.92[ASN][1000 genomes]
rs7167481	0.86[ASN][1000 genomes]
rs732622	0.94[ASN][1000 genomes]
rs938129	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs938130	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	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
8	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

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459600-45469200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:45459800-45471800	Weak transcription	Small Intestine	intestine
3	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
4	chr15:45460000-45465000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:45460000-45465600	Weak transcription	Fetal Intestine Large	intestine
6	chr15:45460000-45465600	Weak transcription	HSMMtube	muscle
7	chr15:45460000-45466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:45460000-45471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:45460000-45471800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:45460000-45472200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
14	chr15:45460200-45467000	Strong transcription	Fetal Intestine Small	intestine
15	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:45460400-45465800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:45460400-45465800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:45460400-45465800	Weak transcription	Lung	lung
19	chr15:45460400-45468600	Weak transcription	Fetal Lung	lung
20	chr15:45460400-45475200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:45460600-45468000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:45460600-45469600	Weak transcription	Placenta	Placenta
23	chr15:45460600-45471800	Weak transcription	Esophagus	oesophagus
24	chr15:45460600-45475400	Weak transcription	Brain Anterior Caudate	brain
25	chr15:45460600-45475600	Weak transcription	Left Ventricle	heart
26	chr15:45460600-45478000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:45460600-45478200	Weak transcription	Adipose Nuclei	Adipose
28	chr15:45461000-45471400	Weak transcription	Stomach Mucosa	stomach
29	chr15:45461200-45466200	Weak transcription	Brain Angular Gyrus	brain
30	chr15:45461200-45471800	Weak transcription	Pancreas	Pancrea
31	chr15:45461200-45473200	Weak transcription	Fetal Brain Male	brain
32	chr15:45461800-45465200	Weak transcription	Spleen	Spleen
33	chr15:45461800-45471800	Strong transcription	Fetal Stomach	stomach
34	chr15:45462200-45477200	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:45462400-45465200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:45462400-45465400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:45462400-45465600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:45462400-45466800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:45462400-45467000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:45462400-45467000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:45462400-45473600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:45462600-45467200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:45462800-45469600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:45462800-45471600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:45462800-45473800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:45463000-45473800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:45463200-45465000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:45463200-45470200	Strong transcription	Ovary	ovary
49	chr15:45463200-45470400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:45463200-45470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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