Variant report

Variant	rs45626633
Chromosome Location	chr1:220440986-220440987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BPNT1-2	chr1:220439327-220441093	NONHSAT009593
2	lnc-BPNT1-2	chr1:220440048-220441259	NONHSAT009595
3	lnc-BPNT1-2	chr1:220439521-220441057	NONHSAT009594

Variant related genes	Relation type
ENSG00000118873	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17007152	0.83[ASN][1000 genomes]
rs17007186	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61830433	0.83[ASN][1000 genomes]
rs61830453	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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	nsv4643	chr1:220397642-220442231	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3452704	chr1:220436224-220441007	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3452705	chr1:220436262-220440993	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv826686	chr1:220439689-220441010	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv945298	chr1:220439798-220441114	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
2	chr1:220416000-220442600	Weak transcription	Fetal Heart	heart
3	chr1:220423000-220443400	Weak transcription	Psoas Muscle	Psoas
4	chr1:220423400-220443400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:220423400-220443400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:220423800-220442600	Weak transcription	Hela-S3	cervix
7	chr1:220425200-220443400	Weak transcription	HUVEC	blood vessel
8	chr1:220426200-220441800	Weak transcription	Small Intestine	intestine
9	chr1:220426600-220443400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:220426600-220443400	Weak transcription	Right Ventricle	heart
11	chr1:220426600-220444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:220426800-220441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:220426800-220441800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:220426800-220442800	Weak transcription	Esophagus	oesophagus
15	chr1:220426800-220443400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:220426800-220443400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:220426800-220443400	Weak transcription	Ovary	ovary
18	chr1:220426800-220444000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:220426800-220444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:220426800-220444400	Weak transcription	Colonic Mucosa	Colon
21	chr1:220426800-220445000	Weak transcription	Aorta	Aorta
22	chr1:220426800-220445000	Weak transcription	Pancreas	Pancrea
23	chr1:220427000-220441400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:220427000-220442800	Weak transcription	Lung	lung
25	chr1:220427000-220443200	Weak transcription	Thymus	Thymus
26	chr1:220427000-220444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:220427000-220445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:220427600-220443400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:220432200-220442400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:220434400-220441200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr1:220434600-220441400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:220434800-220444800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:220435000-220442200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:220435000-220443400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:220435200-220443400	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:220435800-220442200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:220435800-220442800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:220436000-220443200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:220436200-220442400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:220436600-220442400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:220436800-220441200	ZNF genes & repeats	Fetal Brain Female	brain
42	chr1:220436800-220442600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:220437000-220443400	Strong transcription	Primary B cells from cord blood	blood
44	chr1:220437400-220442400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:220437600-220443600	Weak transcription	Fetal Lung	lung
46	chr1:220437800-220441200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:220437800-220443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:220438800-220441200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:220438800-220442400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:220438800-220442600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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