Variant report

Variant	rs3007316
Chromosome Location	chr1:246873394-246873395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246871833..246873688-chr1:246874448..246877432,2	MCF-7	breast:
2	chr1:246867425..246870263-chr1:246871598..246874190,3	MCF-7	breast:
3	chr1:246857655..246865600-chr1:246867157..246874213,9	MCF-7	breast:
4	chr1:246867596..246871068-chr1:246871868..246876366,5	MCF-7	breast:
5	chr1:246869676..246875291-chr1:246885182..246892205,11	MCF-7	breast:
6	chr1:246871057..246874045-chr1:247092351..247094206,2	MCF-7	breast:
7	chr1:246872286..246874686-chr1:246883810..246888250,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10127783	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10159002	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10754532	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10754533	0.86[CHB][hapmap]
rs10802442	0.84[ASN][1000 genomes]
rs10924820	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10924823	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10924824	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12027222	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12085330	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12090470	0.84[ASN][1000 genomes]
rs12122102	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs12132038	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs12144408	0.83[ASN][1000 genomes]
rs12725791	0.84[AMR][1000 genomes]
rs3007307	0.88[AMR][1000 genomes]
rs3007308	0.89[AMR][1000 genomes]
rs3007311	0.81[AMR][1000 genomes]
rs3007312	0.81[AMR][1000 genomes]
rs3007317	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007318	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3007322	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3007323	0.87[ASN][1000 genomes]
rs3007324	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.87[ASN][1000 genomes]
rs3007411	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34649985	0.84[ASN][1000 genomes]
rs34989088	0.81[ASN][1000 genomes]
rs3795463	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3795464	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4130316	0.82[ASN][1000 genomes]
rs4130317	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4244627	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4244630	0.83[ASN][1000 genomes]
rs4926454	0.84[ASN][1000 genomes]
rs4926455	0.82[ASN][1000 genomes]
rs4926457	0.84[ASN][1000 genomes]
rs4926459	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6426323	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs6426326	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6664883	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6685364	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs72764626	0.94[ASN][1000 genomes]
rs7364715	0.89[ASN][1000 genomes]
rs7366377	0.81[ASN][1000 genomes]
rs7416239	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520737	0.85[AMR][1000 genomes]
rs7526537	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs7532928	0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs7532929	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9426213	0.82[AMR][1000 genomes]
rs9426218	0.93[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426269	0.88[ASN][1000 genomes]
rs9426271	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[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
rs3007316	OR2L8	cis	parietal	SCAN
rs3007316	OR2L2	cis	parietal	SCAN
rs3007316	OR2M3	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246866600-246874000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:246870000-246873600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:246870200-246873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:246870800-246873400	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:246870800-246873800	Enhancers	Small Intestine	intestine
6	chr1:246871000-246873800	Enhancers	Primary B cells from cord blood	blood
7	chr1:246871400-246874000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:246872400-246873600	Enhancers	Stomach Mucosa	stomach
9	chr1:246872400-246873800	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:246872400-246873800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:246872400-246873800	Enhancers	Fetal Intestine Small	intestine
12	chr1:246872400-246873800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:246872400-246874000	Enhancers	Fetal Intestine Large	intestine
14	chr1:246872600-246873400	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr1:246872600-246873800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:246872600-246874000	Enhancers	Colonic Mucosa	Colon
17	chr1:246873000-246873400	Enhancers	HepG2	liver
18	chr1:246873000-246874000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:246873200-246873600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:246873200-246874000	Flanking Active TSS	Liver	Liver

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