Variant report

Variant	rs272531
Chromosome Location	chr1:44988433-44988434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44988091..44990441-chr1:45195700..45198117,2	K562	blood:
2	chr1:44987128..44990002-chr1:44991231..44995408,6	K562	blood:
3	chr1:44985539..44988596-chr1:44996958..44999137,3	K562	blood:
4	chr1:44985661..44990504-chr1:44998639..45004929,7	K562	blood:
5	chr1:44986908..44988985-chr1:45186375..45188713,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11577681	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12069261	0.81[JPT][hapmap]
rs12403454	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs16832024	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17386059	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs272532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272533	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746733	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs272531	KLF17	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44979000-44989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:44981000-44988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:44983000-44988600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:44984000-44990200	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:44984400-44990000	Weak transcription	Right Atrium	heart
6	chr1:44984600-44990200	Enhancers	Brain Substantia Nigra	brain
7	chr1:44985400-44988800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:44985400-44989800	Weak transcription	Fetal Thymus	thymus
9	chr1:44986000-44991600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:44987400-44990000	Enhancers	Brain Anterior Caudate	brain
11	chr1:44987400-44990200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:44987400-44992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:44987600-44991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:44987800-44990000	Enhancers	K562	blood
15	chr1:44988000-44989400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:44988000-44989600	Enhancers	Brain Hippocampus Middle	brain
17	chr1:44988000-44990200	Enhancers	Brain Angular Gyrus	brain
18	chr1:44988000-44990600	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:44988000-44990600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:44988200-44990200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:44988200-44990200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:44988400-44989200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr1:44988400-44989400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:44988400-44989400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:44988400-44989600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:44988400-44990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:44988400-44990000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:44988400-44992600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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