Variant report

Variant	rs659131
Chromosome Location	chr7:26881445-26881446
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10257437	0.87[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10259208	0.84[CEU][hapmap]
rs213515	0.93[CEU][hapmap]
rs213516	0.81[CEU][hapmap]
rs213525	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213528	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs213533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213536	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140998	0.81[CEU][hapmap]
rs471536	1.00[JPT][hapmap]
rs477924	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs514043	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558263	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564260	1.00[JPT][hapmap]
rs586947	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs591895	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640512	1.00[JPT][hapmap]
rs668052	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs673502	1.00[JPT][hapmap]
rs688039	1.00[JPT][hapmap]
rs774252	0.87[CEU][hapmap]
rs774265	0.93[CEU][hapmap]
rs7791056	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs659131	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26853400-26882600	Weak transcription	Adipose Nuclei	Adipose
2	chr7:26861000-26882600	Weak transcription	HUVEC	blood vessel
3	chr7:26863200-26893200	Weak transcription	A549	lung
4	chr7:26863600-26894600	Weak transcription	Fetal Intestine Large	intestine
5	chr7:26867200-26897000	Weak transcription	Lung	lung
6	chr7:26869200-26889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:26870000-26884200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:26870000-26885000	Weak transcription	GM12878-XiMat	blood
9	chr7:26870400-26894400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:26870600-26896000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:26871000-26902200	Weak transcription	Dnd41	blood
12	chr7:26871600-26896000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:26872400-26896200	Weak transcription	Fetal Intestine Small	intestine
14	chr7:26872600-26890000	Weak transcription	NHEK	skin
15	chr7:26872600-26894800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:26872800-26892800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:26875200-26889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:26875600-26896000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:26876000-26884000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr7:26876000-26896000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:26876200-26881600	Strong transcription	Primary B cells from cord blood	blood
22	chr7:26876200-26896200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:26876600-26889800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:26877200-26883800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:26877200-26894400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:26877200-26897000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:26877200-26897000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:26877400-26882600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:26877400-26882600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:26877400-26892600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:26877400-26893600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr7:26878000-26883000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:26878000-26883000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:26878000-26892800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:26878600-26889800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:26878800-26893200	Weak transcription	NHLF	lung
37	chr7:26880400-26883800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:26880600-26882400	Weak transcription	NHDF-Ad	bronchial
39	chr7:26880600-26883200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:26880800-26883200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:26881200-26890800	Weak transcription	Liver	Liver
42	chr7:26881200-26892800	Weak transcription	HMEC	breast

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