Variant report

Variant	rs2041809
Chromosome Location	chr2:37013552-37013553
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37011366..37014092-chr2:37310068..37313025,2	K562	blood:
2	chr2:37006258..37010448-chr2:37010681..37014372,3	K562	blood:

Variant related genes	Relation type
ENSG00000008869	Chromatin interaction
ENSG00000152133	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10180537	0.86[CHB][hapmap]
rs10209211	0.88[ASN][1000 genomes]
rs11124543	0.85[ASN][1000 genomes]
rs11124546	0.85[CHB][hapmap]
rs11675969	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs11677279	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs11902881	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs12987048	0.80[CEU][hapmap]
rs1558701	0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs17019851	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs17019854	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs2058683	0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2072527	0.92[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap]
rs3821147	0.84[ASW][hapmap];0.88[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4670169	0.85[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes]
rs4670170	0.88[AMR][1000 genomes]
rs4670615	0.85[ASN][1000 genomes]
rs6544039	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7606098	0.92[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap]
rs763724	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs879613	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs879614	0.80[CEU][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs929640	0.92[CHB][hapmap];0.83[CHD][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	esv1821275	chr2:36991736-37018278	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2041809	EIF2AK2	cis	cerebellum	SCAN
rs2041809	EIF2AK2	cis	parietal	SCAN
rs2041809	HNRPLL	cis	parietal	SCAN
rs2041809	QPCT	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37006000-37014600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:37009800-37016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:37010000-37014000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:37010000-37016000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:37010000-37021600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:37012200-37014000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:37012400-37014400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:37012400-37016400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:37012800-37014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:37012800-37014000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:37012800-37016200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:37012800-37016200	Weak transcription	Fetal Thymus	thymus
13	chr2:37012800-37024800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:37013000-37015600	Weak transcription	Fetal Heart	heart
15	chr2:37013000-37016200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:37013000-37016200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:37013000-37033000	Weak transcription	Ovary	ovary
18	chr2:37013200-37024400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:37013400-37016200	Weak transcription	Primary T cells fromperipheralblood	blood

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