Variant report

Variant	rs2097737
Chromosome Location	chr7:27965088-27965089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10951187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12538288	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1859109	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs191	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs197	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs200	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs201	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs205	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs207	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs208	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs211	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs214	1.00[AFR][1000 genomes]
rs215	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs218	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4722746	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462060	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6951040	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6958293	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6968362	0.83[AMR][1000 genomes]
rs6970113	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6972944	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73083394	0.87[EUR][1000 genomes]
rs7778340	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7783410	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7787507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs916854	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2097737	HOXA2	cis	lung	GTEx

Chromatin state (count:31 , 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	chr7:27961000-27968000	Weak transcription	Brain Substantia Nigra	brain
9	chr7:27961000-27976000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:27961000-27983400	Weak transcription	NH-A	brain
11	chr7:27961400-27967000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:27963200-27968000	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:27963400-27965600	Weak transcription	Left Ventricle	heart
14	chr7:27963400-27967400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:27963400-27978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:27963600-27965400	Weak transcription	Right Atrium	heart
17	chr7:27963600-27968000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:27963600-27970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:27963600-27971800	Weak transcription	Fetal Stomach	stomach
20	chr7:27963600-27975600	Weak transcription	Fetal Heart	heart
21	chr7:27963600-27976400	Weak transcription	Psoas Muscle	Psoas
22	chr7:27963800-27965200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:27963800-27965600	Weak transcription	Primary B cells from cord blood	blood
24	chr7:27963800-27975400	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:27964000-27979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:27964600-27972200	Weak transcription	NHDF-Ad	bronchial
27	chr7:27964600-27973200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:27964600-27975400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:27964800-27973200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:27965000-27965600	Enhancers	GM12878-XiMat	blood
31	chr7:27965000-27967800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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