Variant report

Variant	rs270716
Chromosome Location	chr1:45054866-45054867
allele	A/G
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	chr1:45052900..45054995-chr1:45056850..45058770,2	K562	blood:
2	chr1:45044310..45046811-chr1:45054815..45057295,2	K562	blood:
3	chr1:45053513..45056488-chr1:45158048..45160524,2	K562	blood:
4	chr1:45053495..45055636-chr1:45056850..45058814,2	K562	blood:
5	chr1:45043721..45045810-chr1:45054815..45057693,2	K562	blood:
6	chr1:45054153..45057200-chr1:45115881..45118769,3	K562	blood:
7	chr1:45050697..45052579-chr1:45054486..45057426,3	K562	blood:
8	chr1:44500355..44502948-chr1:45053577..45055630,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230615	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs156651	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs156652	0.90[ASN][1000 genomes]
rs270703	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs270707	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270708	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270709	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270710	0.90[ASN][1000 genomes]
rs270711	0.90[ASN][1000 genomes]
rs270712	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270713	0.90[ASN][1000 genomes]
rs270714	0.90[ASN][1000 genomes]
rs270719	0.89[ASN][1000 genomes]
rs272529	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs275079	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6429543	0.94[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270716	LEPRE1	cis	parietal	SCAN
rs270716	PLK3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45047800-45060000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45049000-45062800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:45050000-45057600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:45051600-45057200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:45052000-45057200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:45052400-45057600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:45053000-45055600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:45053000-45059000	Enhancers	Brain Substantia Nigra	brain
10	chr1:45053200-45055000	Enhancers	Brain Angular Gyrus	brain
11	chr1:45053200-45055000	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:45053200-45055000	Enhancers	Fetal Intestine Large	intestine
13	chr1:45053200-45055000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
14	chr1:45053200-45063600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:45053600-45055000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:45053600-45055000	Enhancers	Fetal Intestine Small	intestine
17	chr1:45054000-45055000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:45054000-45056000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:45054200-45055600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:45054200-45055600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:45054200-45057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:45054200-45057600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:45054400-45055400	Weak transcription	Brain Anterior Caudate	brain

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