Variant report

Variant	rs12987048
Chromosome Location	chr2:37024713-37024714
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	chr2:37019404..37022221-chr2:37024181..37026329,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1014584	0.89[MEX][hapmap]
rs11124544	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675969	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs11677279	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041809	0.80[CEU][hapmap]
rs2276669	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2372713	1.00[CHD][hapmap]
rs3821147	0.84[CEU][hapmap]
rs4670169	0.88[CEU][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs4670170	0.91[EUR][1000 genomes]
rs4670612	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670613	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670614	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4670615	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7606098	0.83[MEX][hapmap]
rs879614	0.84[CEU][hapmap];0.84[MEX][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv2682	chr2:37015550-37060432	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12987048	EIF2AK2	cis	cerebellum	SCAN
rs12987048	CGRRF1	trans	parietal	SCAN
rs12987048	EIF2AK2	cis	parietal	SCAN
rs12987048	QPCT	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37012800-37024800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:37013000-37033000	Weak transcription	Ovary	ovary
3	chr2:37022200-37027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:37024400-37024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr2:37024400-37024800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:37024400-37025000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:37024400-37025000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:37024400-37025000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:37024400-37025200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:37024400-37025400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:37024400-37025400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:37024400-37028400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:37024400-37033800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:37024600-37025000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:37024600-37025000	Enhancers	Fetal Thymus	thymus
16	chr2:37024600-37025200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:37024600-37025200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr2:37024600-37025200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr2:37024600-37025200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:37024600-37025800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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