Variant report

Variant	rs17269154
Chromosome Location	chr2:58872235-58872236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58868791..58870699-chr2:58870804..58872646,2	MCF-7	breast:
2	chr2:58871708..58873998-chr2:58879181..58880862,2	K562	blood:
3	chr2:58871707..58873924-chr2:58875799..58878057,2	K562	blood:
4	chr2:58863044..58865582-chr2:58870995..58873370,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10490092	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10490093	0.98[EUR][1000 genomes]
rs13026438	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13421824	0.98[EUR][1000 genomes]
rs17049642	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17190597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17190618	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17269182	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17549476	0.98[EUR][1000 genomes]
rs17549656	0.94[EUR][1000 genomes]
rs17549677	0.97[EUR][1000 genomes]
rs17549712	0.98[EUR][1000 genomes]
rs17549754	0.95[EUR][1000 genomes]
rs17549803	0.95[EUR][1000 genomes]
rs17614872	0.99[EUR][1000 genomes]
rs17614895	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17615036	0.92[EUR][1000 genomes]
rs17615120	0.97[EUR][1000 genomes]
rs17615185	0.95[EUR][1000 genomes]
rs17615279	0.95[EUR][1000 genomes]
rs17615309	0.95[EUR][1000 genomes]
rs17615381	0.95[EUR][1000 genomes]
rs1922781	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1950160	0.98[EUR][1000 genomes]
rs2204913	0.96[EUR][1000 genomes]
rs55645922	0.98[EUR][1000 genomes]
rs55745617	0.98[EUR][1000 genomes]
rs56174720	0.97[EUR][1000 genomes]
rs56266136	0.98[EUR][1000 genomes]
rs56365214	0.97[EUR][1000 genomes]
rs60018257	0.95[EUR][1000 genomes]
rs7419776	0.87[ASN][1000 genomes]
rs984881	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs984882	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs984883	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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	nsv1012213	chr2:58671881-58893730	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv535736	chr2:58671881-58893730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv431180	chr2:58857542-59178687	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17269154	LOC339803	cis	parietal	SCAN
rs17269154	SPTBN1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58859200-58875000	Weak transcription	Fetal Brain Male	brain
2	chr2:58866400-58879000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:58871800-58872800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:58872000-58872400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:58872000-58872400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:58872000-58872400	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:58872000-58872400	Enhancers	K562	blood
8	chr2:58872000-58872600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr2:58872000-58872600	Enhancers	Fetal Brain Female	brain
10	chr2:58872200-58872400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:58872200-58872600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:58872200-58872600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:58872200-58872600	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:58872200-58872600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:58872200-58873600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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