Variant report

Variant	rs3007324
Chromosome Location	chr1:246914940-246914941
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246901571..246903132-chr1:246912422..246914944,2	K562	blood:
2	chr1:246886819..246888757-chr1:246914269..246916145,2	MCF-7	breast:
3	chr1:246911249..246913997-chr1:246914503..246916490,2	K562	blood:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10127783	0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10159002	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10754532	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10754533	0.81[CHB][hapmap]
rs10802442	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10924820	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10924823	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10924824	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12027222	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12085330	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12090470	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12122102	1.00[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[YRI][hapmap]
rs12132038	1.00[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap]
rs12142760	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12144408	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3007316	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]
rs3007317	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3007318	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007319	1.00[YRI][hapmap]
rs3007322	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007323	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007411	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34649985	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34989088	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3795463	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3795464	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4130316	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4130317	0.92[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244627	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4244630	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4926454	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4926455	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4926457	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4926459	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6426323	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs6426326	0.85[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664883	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6685364	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72764626	0.93[ASN][1000 genomes]
rs7364715	0.97[ASN][1000 genomes]
rs7365076	0.86[ASN][1000 genomes]
rs7366377	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7416239	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532928	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs9426218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9426269	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3007324	OR2M2	cis	cerebellum	SCAN
rs3007324	OR2L2	cis	parietal	SCAN
rs3007324	CNST	cis	cerebellum	SCAN
rs3007324	OR2L8	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
6	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
8	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
12	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:246903000-246917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:246905000-246922200	Weak transcription	Brain Germinal Matrix	brain
17	chr1:246905000-246922200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:246905000-246923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:246905000-246923800	Weak transcription	Thymus	Thymus
20	chr1:246905000-246924000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
22	chr1:246905600-246923400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:246905600-246923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:246905800-246923800	Weak transcription	Colonic Mucosa	Colon
25	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:246906000-246923800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:246906200-246917200	Weak transcription	GM12878-XiMat	blood
28	chr1:246906800-246923000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:246906800-246923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:246907000-246923600	Weak transcription	Aorta	Aorta
31	chr1:246907400-246922200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:246908600-246923400	Weak transcription	NH-A	brain
33	chr1:246908600-246923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:246908800-246922200	Weak transcription	Brain Substantia Nigra	brain
35	chr1:246908800-246922600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:246908800-246922600	Weak transcription	NHLF	lung
37	chr1:246908800-246923000	Weak transcription	HUVEC	blood vessel
38	chr1:246908800-246923600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:246908800-246923600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:246908800-246923800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:246909000-246916800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:246909000-246918600	Weak transcription	HSMM	muscle
43	chr1:246909000-246922400	Weak transcription	Fetal Kidney	kidney
44	chr1:246909000-246922400	Weak transcription	NHDF-Ad	bronchial
45	chr1:246909000-246922600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:246909000-246922600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:246909000-246923600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:246909000-246923600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:246909000-246923800	Weak transcription	Brain Angular Gyrus	brain
50	chr1:246909200-246922400	Weak transcription	Brain Anterior Caudate	brain

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