Variant report

Variant	rs1024453
Chromosome Location	chr7:26763002-26763003
allele	C/T
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:28)

rs_ID	r²[population]
rs1024452	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129771	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971041	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971098	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972823	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973332	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976472	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978456	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979611	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982489	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213515	1.00[JPT][hapmap]
rs2189016	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs57579189	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57687803	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61609910	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945204	0.89[EUR][1000 genomes]
rs6967749	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970475	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73683491	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683496	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683510	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763616	0.83[AFR][1000 genomes]
rs774265	1.00[JPT][hapmap]
rs7777645	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780206	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799519	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802688	0.85[AFR][1000 genomes]
rs7809419	0.80[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018125	chr7:26745074-26789814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1024453	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26731800-26779200	Weak transcription	Spleen	Spleen
2	chr7:26732200-26765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:26740400-26782400	Weak transcription	Fetal Intestine Small	intestine
4	chr7:26745000-26780800	Weak transcription	Aorta	Aorta
5	chr7:26745400-26764600	Weak transcription	Adipose Nuclei	Adipose
6	chr7:26745800-26764600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:26746200-26780600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:26746600-26777400	Weak transcription	Lung	lung
9	chr7:26748000-26764800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:26749200-26779600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:26749600-26781000	Weak transcription	NHEK	skin
12	chr7:26750400-26812000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:26753600-26782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:26754200-26780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:26754400-26782400	Weak transcription	Fetal Stomach	stomach
16	chr7:26754600-26780200	Weak transcription	NHLF	lung
17	chr7:26754800-26777000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:26754800-26783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:26755600-26782400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:26756200-26776800	Weak transcription	Dnd41	blood
21	chr7:26756600-26780600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:26756800-26763600	Weak transcription	Gastric	stomach
23	chr7:26758400-26767200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr7:26758400-26780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:26758600-26767400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:26759400-26775800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:26760200-26765000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:26760400-26765400	Weak transcription	Primary B cells from cord blood	blood
29	chr7:26760800-26763600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:26761000-26763400	Weak transcription	Hela-S3	cervix
31	chr7:26761600-26766800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:26762200-26763200	Enhancers	Fetal Muscle Trunk	muscle
33	chr7:26762600-26763200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr7:26762600-26763800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:26762800-26763200	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:26762800-26763200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr7:26762800-26763200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:26762800-26763200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:26762800-26763200	Enhancers	Fetal Muscle Leg	muscle
40	chr7:26762800-26765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:26763000-26777600	Weak transcription	Fetal Lung	lung
42	chr7:26763000-26780600	Weak transcription	Primary T cells from cord blood	blood

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