Variant report

Variant	rs270724
Chromosome Location	chr1:44991278-44991279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44990153..44991798-chr1:45185234..45187477,2	K562	blood:
2	chr1:44990298..44993121-chr1:45185503..45187477,2	K562	blood:
3	chr1:44987128..44990002-chr1:44991231..44995408,6	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12122791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132722	0.96[GIH][hapmap]
rs12138940	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12145658	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12740646	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4660811	1.00[YRI][hapmap]
rs55897190	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72895565	0.93[EUR][1000 genomes]
rs7550459	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270724	RNF220	cis	parietal	SCAN
rs270724	KCNQ4	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44986000-44991600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:44987400-44992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:44987600-44991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:44988400-44992600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:44989000-44991400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:44989200-44991400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr1:44989800-44992800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:44990400-44991400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:44990400-44991600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:44990600-44991400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:44990600-44991400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:44990600-44991400	Enhancers	Fetal Lung	lung
13	chr1:44990600-44991400	Enhancers	Right Ventricle	heart
14	chr1:44990600-44991600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:44990600-44991600	Enhancers	Fetal Heart	heart
16	chr1:44990600-44992000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:44990600-44992000	Enhancers	Brain Cingulate Gyrus	brain
18	chr1:44990600-44992000	Bivalent Enhancer	Fetal Stomach	stomach
19	chr1:44990600-44992800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:44990600-44993000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:44990600-44997000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:44990800-44991400	Enhancers	Placenta	Placenta
23	chr1:44990800-44991600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:44990800-44992000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:44990800-44992000	Enhancers	Brain Hippocampus Middle	brain
26	chr1:44990800-44992400	Enhancers	K562	blood
27	chr1:44990800-44992800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:44990800-44993000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:44991000-44991600	Enhancers	Brain Angular Gyrus	brain
30	chr1:44991000-44992200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:44991000-44992200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:44991000-44992400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr1:44991000-44992400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:44991000-44992400	Enhancers	Brain Substantia Nigra	brain
35	chr1:44991000-44992800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:44991000-44992800	Enhancers	Brain Anterior Caudate	brain
37	chr1:44991200-44991400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:44991200-44992200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:44991200-44992600	Enhancers	H9 Cell Line	embryonic stem cell
40	chr1:44991200-44992600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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