Variant report

Variant	rs354236
Chromosome Location	chr2:54962829-54962830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54951102..54953008-chr2:54959664..54962831,3	K562	blood:

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1047499	0.81[TSI][hapmap]
rs11898012	0.86[TSI][hapmap]
rs12105792	0.84[TSI][hapmap]
rs13016942	0.84[TSI][hapmap]
rs1367295	0.86[TSI][hapmap]
rs168503	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs168507	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs168508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344072	0.84[TSI][hapmap]
rs17416806	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs181348	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821138	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187124	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs191628	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2567835	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2941595	0.86[TSI][hapmap]
rs2971875	0.81[EUR][1000 genomes]
rs2971877	0.81[TSI][hapmap]
rs2971879	0.86[TSI][hapmap]
rs2971889	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs354187	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs354195	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs354197	0.81[EUR][1000 genomes]
rs354209	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs354214	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs354231	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs354237	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs354238	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs354243	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671226	0.84[TSI][hapmap]
rs4671956	0.84[TSI][hapmap]
rs4671960	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs4671961	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs58175244	0.91[ASN][1000 genomes]
rs6729826	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv582025	chr2:54960680-54973834	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs354236	SPTBN1	cis	multi-tissue	Pritchard
rs354236	RSRC1	trans	cerebellum	SCAN
rs354236	ACYP2	cis	parietal	SCAN
rs354236	SPTBN1	cis	cerebellum	SCAN
rs354236	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54954600-54965000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:54956800-54964800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:54956800-54964800	Weak transcription	HepG2	liver
4	chr2:54962600-54963400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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