Variant report

Variant	rs3935813
Chromosome Location	chr5:54140334-54140335
allele	C/T
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: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10042288	0.88[EUR][1000 genomes]
rs10042495	0.88[EUR][1000 genomes]
rs10042734	0.85[EUR][1000 genomes]
rs10056452	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10058862	0.91[EUR][1000 genomes]
rs10805469	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10805470	0.83[EUR][1000 genomes]
rs10940431	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10940432	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10940434	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11738151	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11742711	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12515327	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12657845	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13186826	0.80[AMR][1000 genomes]
rs1560165	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1560166	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17588816	0.83[EUR][1000 genomes]
rs1965716	0.85[EUR][1000 genomes]
rs1991498	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2017082	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2019005	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2195392	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2195393	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28564901	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2897758	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3916738	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4074332	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4242047	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4315891	0.89[ASN][1000 genomes]
rs4373237	0.91[ASN][1000 genomes]
rs4407587	0.89[ASN][1000 genomes]
rs4446420	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4502767	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4865586	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4865587	0.90[ASN][1000 genomes]
rs4865879	0.83[EUR][1000 genomes]
rs4865880	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4865882	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6860824	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6863705	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs6891667	1.00[ASN][1000 genomes]
rs6893903	0.96[ASN][1000 genomes]
rs734097	0.84[EUR][1000 genomes]
rs737526	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7448996	1.00[ASN][1000 genomes]
rs7708368	0.86[ASN][1000 genomes]
rs7709516	0.83[EUR][1000 genomes]
rs976645	0.83[AMR][1000 genomes];0.86[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
rs3935813	ARL15	cis	cerebellum	SCAN

Chromatin state (count:27 , 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	chr5:54135000-54140400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:54135800-54140800	Weak transcription	Fetal Intestine Large	intestine
6	chr5:54136000-54140800	Weak transcription	Liver	Liver
7	chr5:54137200-54140800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:54138400-54142000	Enhancers	NHLF	lung
9	chr5:54138600-54140800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:54138800-54140400	Weak transcription	Aorta	Aorta
11	chr5:54139600-54140800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:54139600-54140800	Enhancers	NHDF-Ad	bronchial
13	chr5:54139600-54142000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:54139800-54140400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:54139800-54140800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:54140000-54141600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:54140000-54141800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:54140200-54140400	Enhancers	Brain Substantia Nigra	brain
19	chr5:54140200-54140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:54140200-54140600	Enhancers	HSMM	muscle
21	chr5:54140200-54140800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:54140200-54140800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:54140200-54140800	Enhancers	Fetal Kidney	kidney
24	chr5:54140200-54140800	Enhancers	Ovary	ovary
25	chr5:54140200-54141000	Enhancers	NH-A	brain
26	chr5:54140200-54141200	Enhancers	Primary B cells from cord blood	blood
27	chr5:54140200-54141800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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