Variant report

Variant	rs2493824
Chromosome Location	chr1:227627663-227627664
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227502515..227505925-chr1:227623984..227628768,4	K562	blood:
2	chr1:227626622..227628600-chr1:227629943..227632717,2	K562	blood:
3	chr1:227499595..227501677-chr1:227627472..227629902,2	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10916145	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11586581	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11799974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2644141	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814087	0.92[AFR][1000 genomes]
rs2819513	0.83[AFR][1000 genomes]
rs2819515	0.83[AFR][1000 genomes]
rs7546172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2493824	AIDA	cis	cerebellum	SCAN
rs2493824	RNF187	cis	parietal	SCAN
rs2493824	HIST3H3	cis	cerebellum	SCAN
rs2493824	PSEN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227617600-227631200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:227619600-227628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:227625000-227628600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:227625600-227627800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:227625600-227627800	Weak transcription	HUVEC	blood vessel
6	chr1:227625600-227628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227625600-227628200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:227625600-227628400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:227625600-227628600	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:227625600-227628600	Weak transcription	Left Ventricle	heart
11	chr1:227625600-227628800	Weak transcription	Right Ventricle	heart
12	chr1:227625600-227629800	Weak transcription	Fetal Heart	heart
13	chr1:227625600-227631600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:227625600-227632000	Weak transcription	Fetal Kidney	kidney
15	chr1:227625800-227627800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:227625800-227627800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:227625800-227628200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:227625800-227628600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:227625800-227628600	Weak transcription	HSMM	muscle
20	chr1:227625800-227630600	Weak transcription	Brain Angular Gyrus	brain
21	chr1:227626000-227628800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:227627600-227627800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:227627600-227628800	Enhancers	Brain Anterior Caudate	brain
24	chr1:227627600-227629000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:227627600-227629000	Enhancers	Adipose Nuclei	Adipose
26	chr1:227627600-227629000	Enhancers	Brain Hippocampus Middle	brain
27	chr1:227627600-227629000	Enhancers	K562	blood
28	chr1:227627600-227629200	Enhancers	Brain Substantia Nigra	brain
29	chr1:227627600-227629200	Enhancers	Ovary	ovary
30	chr1:227627600-227630000	Enhancers	Right Atrium	heart

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