Variant report

Variant	rs4683588
Chromosome Location	chr3:140969254-140969255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140966461..140969300-chr3:140987010..140989474,2	MCF-7	breast:
2	chr3:140966619..140969493-chr3:140970424..140973132,3	MCF-7	breast:
3	chr3:140960166..140963166-chr3:140967948..140970939,3	MCF-7	breast:
4	chr3:140965310..140966994-chr3:140967506..140969664,2	MCF-7	breast:
5	chr3:140967710..140969385-chr3:140973413..140974943,2	K562	blood:
6	chr3:140968757..140971307-chr3:140972187..140974906,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11715472	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1511376	0.93[CEU][hapmap]
rs1511377	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1511378	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs1511386	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs17204236	1.00[MKK][hapmap]
rs17787670	1.00[LWK][hapmap]
rs1877219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983234	1.00[LWK][hapmap]
rs1993904	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs2169868	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2311734	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683398	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4683592	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6439984	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6439985	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6439990	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6439993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803826	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs7629077	0.80[EUR][1000 genomes]
rs7643346	0.87[GIH][hapmap]
rs899349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289627	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs9841326	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs9878866	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9880195	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4683588	OR2A12	trans	parietal	SCAN
rs4683588	RNF7	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:140957800-140973600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:140960800-140969800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:140961000-140978800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:140961200-140973600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
13	chr3:140961400-140969400	Weak transcription	HSMMtube	muscle
14	chr3:140961400-140974200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:140961400-140974200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:140961400-140974400	Weak transcription	Placenta	Placenta
17	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:140961600-140971400	Weak transcription	Fetal Brain Female	brain
19	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:140962200-140974200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:140962400-140977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:140962600-140969800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:140962600-140971600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:140962600-140974200	Weak transcription	Spleen	Spleen
26	chr3:140962600-140974600	Weak transcription	Right Atrium	heart
27	chr3:140962600-140975000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:140962600-140978800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
30	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:140962800-140969400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:140962800-140971000	Weak transcription	Fetal Intestine Small	intestine
33	chr3:140962800-140971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
35	chr3:140963600-140978800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:140963800-140970000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:140964800-140978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:140965000-140970000	Weak transcription	Primary T cells from cord blood	blood
39	chr3:140965400-140971600	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
41	chr3:140966200-140974200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
43	chr3:140967000-140971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:140968000-140969800	Weak transcription	Fetal Heart	heart
45	chr3:140968000-140976600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:140968200-140969400	Weak transcription	Esophagus	oesophagus
47	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:140968200-140990000	Weak transcription	Gastric	stomach
49	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
50	chr3:140968600-140971600	Weak transcription	Fetal Brain Male	brain

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