Variant report

Variant	rs11693755
Chromosome Location	chr2:56245554-56245555
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	chr2:55993449..55995609-chr2:56244406..56246687,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10171335	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194204	1.00[ASN][1000 genomes]
rs10194401	1.00[ASN][1000 genomes]
rs10200414	1.00[ASN][1000 genomes]
rs10206522	1.00[ASN][1000 genomes]
rs10206619	1.00[ASN][1000 genomes]
rs10210936	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686318	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901093	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12713312	1.00[ASN][1000 genomes]
rs12713313	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713314	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991457	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023665	0.81[EUR][1000 genomes]
rs13029542	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13398053	1.00[ASN][1000 genomes]
rs13399945	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410155	1.00[ASN][1000 genomes]
rs13431392	1.00[ASN][1000 genomes]
rs13432828	1.00[ASN][1000 genomes]
rs1347093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835897	1.00[ASN][1000 genomes]
rs2009613	0.82[CEU][hapmap]
rs2868992	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34561537	1.00[ASN][1000 genomes]
rs4553860	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545539	0.94[ASN][1000 genomes]
rs6724635	1.00[ASN][1000 genomes]
rs6724872	1.00[ASN][1000 genomes]
rs6741589	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745615	1.00[ASN][1000 genomes]
rs6756818	1.00[ASN][1000 genomes]
rs7557630	1.00[ASN][1000 genomes]
rs7587002	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597360	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601814	1.00[ASN][1000 genomes]
rs9967780	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	nsv520175	chr2:56228351-56331375	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11693755	SMEK2	cis	cerebellum	SCAN
rs11693755	C2orf63	cis	cerebellum	SCAN
rs11693755	GPR75	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56243200-56246400	Enhancers	HUVEC	blood vessel
2	chr2:56243400-56247000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:56243600-56247600	Weak transcription	A549	lung
4	chr2:56243600-56248200	Weak transcription	Fetal Kidney	kidney
5	chr2:56244800-56245600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr2:56244800-56246000	Enhancers	Hela-S3	cervix
7	chr2:56245400-56245600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:56245400-56245600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:56245400-56245600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:56245400-56245600	Enhancers	Adipose Nuclei	Adipose
11	chr2:56245400-56245600	Enhancers	Brain Germinal Matrix	brain
12	chr2:56245400-56245600	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr2:56245400-56245600	Flanking Active TSS	Pancreas	Pancrea
14	chr2:56245400-56245800	Enhancers	Fetal Muscle Leg	muscle
15	chr2:56245400-56246000	Active TSS	Brain Hippocampus Middle	brain

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