Variant report

Variant	rs12403454
Chromosome Location	chr1:45000436-45000437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44999691..45002085-chr1:45187157..45188698,2	K562	blood:
2	chr1:44999769..45001806-chr1:45008456..45010652,2	K562	blood:
3	chr1:44999941..45002884-chr1:45004483..45007957,3	K562	blood:
4	chr1:44985661..44990504-chr1:44998639..45004929,7	K562	blood:
5	chr1:44999091..45001441-chr1:45003471..45005983,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11577681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065045	0.92[GIH][hapmap]
rs16832024	1.00[CHB][hapmap]
rs17386059	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs272531	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs272533	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs28522772	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3896232	0.83[CEU][hapmap];0.92[GIH][hapmap]
rs746733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs12403454	ELOVL1	cis	parietal	SCAN
rs12403454	TCTEX1D4	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44992200-45000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:44996200-45004400	Enhancers	Brain Substantia Nigra	brain
3	chr1:44996800-45001600	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:44997000-45004200	Enhancers	Brain Angular Gyrus	brain
5	chr1:44998600-45000600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:44998800-45001400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:44998800-45001400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:44998800-45001600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:44998800-45001800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:44998800-45002000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:44998800-45002000	Weak transcription	Stomach Mucosa	stomach
12	chr1:44998800-45004400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:44998800-45006600	Enhancers	Brain Hippocampus Middle	brain
14	chr1:44998800-45017800	Weak transcription	Right Atrium	heart
15	chr1:44998800-45022000	Weak transcription	HepG2	liver
16	chr1:44999000-45001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:44999000-45001600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:44999000-45001800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:44999000-45005400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:44999800-45001000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:45000000-45002200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:45000200-45000600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:45000200-45000600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr1:45000200-45002800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:45000200-45002800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:45000200-45004200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:45000200-45008200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:45000400-45000600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:45000400-45000600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr1:45000400-45001200	Weak transcription	Brain Anterior Caudate	brain

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