Variant report

Variant	rs3935814
Chromosome Location	chr5:54140573-54140574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53813794..53815703-chr5:54138497..54141381,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13156560	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13173142	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13183019	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13183813	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34211924	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34503985	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34563029	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34619620	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34728968	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35046115	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35409466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35805787	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35839938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35985754	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36000196	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36009662	0.95[EUR][1000 genomes]
rs3935815	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4301189	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4425466	0.95[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs4565175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4572962	0.90[CEU][hapmap]
rs55903850	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66525543	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66928876	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66955270	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67500010	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7733091	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935814	ITGA2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54131000-54140800	Weak transcription	Adipose Nuclei	Adipose
2	chr5:54132000-54140800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:54133800-54140600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr5:54135800-54140800	Weak transcription	Fetal Intestine Large	intestine
5	chr5:54136000-54140800	Weak transcription	Liver	Liver
6	chr5:54137200-54140800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:54138400-54142000	Enhancers	NHLF	lung
8	chr5:54138600-54140800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:54139600-54140800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:54139600-54140800	Enhancers	NHDF-Ad	bronchial
11	chr5:54139600-54142000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:54139800-54140800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:54140000-54141600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:54140000-54141800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:54140200-54140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:54140200-54140600	Enhancers	HSMM	muscle
17	chr5:54140200-54140800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:54140200-54140800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:54140200-54140800	Enhancers	Fetal Kidney	kidney
20	chr5:54140200-54140800	Enhancers	Ovary	ovary
21	chr5:54140200-54141000	Enhancers	NH-A	brain
22	chr5:54140200-54141200	Enhancers	Primary B cells from cord blood	blood
23	chr5:54140200-54141800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:54140400-54140600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:54140400-54140600	Enhancers	Fetal Stomach	stomach
26	chr5:54140400-54141000	Enhancers	Aorta	Aorta
27	chr5:54140400-54141000	Active TSS	Colonic Mucosa	Colon
28	chr5:54140400-54141200	Active TSS	Brain Substantia Nigra	brain
29	chr5:54140400-54141800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:54140400-54141800	Enhancers	Osteobl	bone
31	chr5:54140400-54142000	Enhancers	HSMMtube	muscle

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