Variant report

Variant	rs7554123
Chromosome Location	chr1:45004204-45004205
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:44985661..44990504-chr1:44998639..45004929,7	K562	blood:
2	chr1:44999091..45001441-chr1:45003471..45005983,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12032873	0.81[GIH][hapmap]
rs7532058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7554123	EGR2	trans	brain	seeQTL
rs7554123	HBG1	trans	brain	seeQTL
rs7554123	CCL3	trans	brain	seeQTL
rs7554123	CCL4	trans	brain	seeQTL
rs7554123	HBG2	trans	brain	seeQTL
rs7554123	FOSB	trans	brain	seeQTL
rs7554123	PTGS2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44996200-45004400	Enhancers	Brain Substantia Nigra	brain
2	chr1:44998800-45004400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:44998800-45006600	Enhancers	Brain Hippocampus Middle	brain
4	chr1:44998800-45017800	Weak transcription	Right Atrium	heart
5	chr1:44998800-45022000	Weak transcription	HepG2	liver
6	chr1:44999000-45005400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:45000200-45008200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:45001000-45004400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr1:45001400-45006000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45001800-45006600	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:45002200-45005000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:45002400-45005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:45002400-45005200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:45002400-45005400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:45002600-45004400	Enhancers	Stomach Mucosa	stomach
16	chr1:45002600-45005000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:45002600-45005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:45003000-45004400	Enhancers	Fetal Intestine Small	intestine
19	chr1:45003200-45004400	Enhancers	Fetal Intestine Large	intestine
20	chr1:45003600-45005000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:45003600-45007800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:45003800-45005400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:45004200-45004800	Weak transcription	Brain Angular Gyrus	brain
24	chr1:45004200-45005200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:45004200-45005200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:45004200-45005400	Weak transcription	Brain Anterior Caudate	brain
27	chr1:45004200-45005600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:45004200-45005600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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