Variant report

Variant	rs7532928
Chromosome Location	chr1:246870293-246870294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10127783	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs10159002	0.87[CHB][hapmap]
rs10754532	0.87[CHB][hapmap];0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs10924820	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs10924823	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs10924824	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs12085330	0.87[CHB][hapmap]
rs12122102	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs12132038	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs12725791	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3007307	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3007308	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3007309	0.86[EUR][1000 genomes]
rs3007310	0.90[EUR][1000 genomes]
rs3007311	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3007312	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3007313	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007316	0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3007317	0.88[ASN][1000 genomes]
rs3007318	0.83[ASN][1000 genomes]
rs3007322	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs3007323	0.81[ASN][1000 genomes]
rs3007324	0.81[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs3007411	0.85[ASN][1000 genomes]
rs3795463	0.86[CHB][hapmap]
rs3795464	0.87[CHB][hapmap]
rs4130317	0.87[CHD][hapmap]
rs4244627	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs4926459	0.87[CHB][hapmap]
rs6426322	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6426323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426326	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs6664883	0.87[CHB][hapmap]
rs6685364	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs72764626	0.87[ASN][1000 genomes]
rs7364715	0.83[ASN][1000 genomes]
rs7416239	0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs7520737	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7526537	0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426213	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9426218	0.81[CHB][hapmap]
rs9426269	0.82[ASN][1000 genomes]
rs9426271	0.80[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7532928	OR2M3	cis	parietal	SCAN
rs7532928	OR2L2	cis	parietal	SCAN
rs7532928	OR2M2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246862600-246872800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:246862800-246871000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:246863000-246871000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:246866600-246874000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:246867400-246871000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:246867400-246872400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:246867400-246872600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:246867600-246870800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:246867800-246870800	Weak transcription	Dnd41	blood
10	chr1:246868000-246870400	Weak transcription	Stomach Mucosa	stomach
11	chr1:246868000-246870800	Weak transcription	Small Intestine	intestine
12	chr1:246869000-246871000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:246869200-246870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:246869200-246871200	Weak transcription	NHLF	lung
15	chr1:246869400-246870600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:246869400-246871000	Weak transcription	Osteobl	bone
17	chr1:246869800-246872600	Enhancers	HepG2	liver
18	chr1:246869800-246873200	Enhancers	Liver	Liver
19	chr1:246870000-246870400	Enhancers	Fetal Intestine Large	intestine
20	chr1:246870000-246871000	Weak transcription	Hela-S3	cervix
21	chr1:246870000-246871000	Weak transcription	NHDF-Ad	bronchial
22	chr1:246870000-246871600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:246870000-246872600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:246870000-246873600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:246870200-246870600	Weak transcription	Placenta	Placenta
26	chr1:246870200-246871000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:246870200-246871400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:246870200-246871400	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:246870200-246873200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:246870200-246873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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