Variant report

Variant	rs2040666
Chromosome Location	chr7:27968193-27968194
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	chr7:27967354..27970328-chr7:27973178..27975197,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11760913	0.86[CHB][hapmap]
rs17621988	0.81[CEU][hapmap]
rs17622746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17622806	0.94[CEU][hapmap];0.86[CHB][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1989908	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs1989909	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs28566774	0.81[EUR][1000 genomes]
rs34118973	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34269971	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3919460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67716336	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68104887	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6968704	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs7776540	0.94[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7783465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9801472	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2040666	FKBP14	cis	cerebellum	SCAN
rs2040666	HOXA10	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:27956600-27979800	Weak transcription	Aorta	Aorta
4	chr7:27957200-27979000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:27957600-27969200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:27957800-27973400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:27961000-27976000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:27961000-27983400	Weak transcription	NH-A	brain
10	chr7:27963400-27978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:27963600-27970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:27963600-27971800	Weak transcription	Fetal Stomach	stomach
13	chr7:27963600-27975600	Weak transcription	Fetal Heart	heart
14	chr7:27963600-27976400	Weak transcription	Psoas Muscle	Psoas
15	chr7:27963800-27975400	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:27964000-27979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:27964600-27972200	Weak transcription	NHDF-Ad	bronchial
18	chr7:27964600-27973200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:27964600-27975400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:27964800-27973200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:27966400-27976600	Weak transcription	Primary B cells from cord blood	blood
22	chr7:27966600-27975400	Weak transcription	Left Ventricle	heart
23	chr7:27967000-27971800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:27967400-27968200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:27967800-27970800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:27968000-27968400	Enhancers	Brain Cingulate Gyrus	brain
27	chr7:27968000-27969000	Enhancers	Brain Angular Gyrus	brain
28	chr7:27968000-27969200	Enhancers	Brain Substantia Nigra	brain
29	chr7:27968000-27969200	Enhancers	Colon Smooth Muscle	Colon
30	chr7:27968000-27969200	Enhancers	Skeletal Muscle Female	skeletal muscle

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