Variant report

Variant	rs12145674
Chromosome Location	chr1:221000273-221000274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10495152	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863567	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863568	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118609	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118611	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118615	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118616	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118619	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590678	0.84[ASN][1000 genomes]
rs12057411	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073837	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12089958	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12117818	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124030	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12129004	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12139139	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141189	0.80[CEU][hapmap]
rs1335919	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1494368	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1494371	0.81[EUR][1000 genomes]
rs1494372	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008806	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17596850	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597773	0.80[CEU][hapmap]
rs17650107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242358	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs2279638	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378425	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2642421	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs35730037	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143773	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61830270	0.90[ASN][1000 genomes]
rs61830289	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6541161	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668666	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673877	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693017	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7530074	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530176	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530493	0.98[ASN][1000 genomes]
rs7544735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553447	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881995	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903319	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs984676	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12145674	BPNT1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220980400-221001400	Weak transcription	Gastric	stomach
2	chr1:220984200-221001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:220984600-221006600	Weak transcription	Psoas Muscle	Psoas
4	chr1:220987600-221003800	Weak transcription	HepG2	liver
5	chr1:220989800-221000800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:220990000-221001200	Weak transcription	Hela-S3	cervix
7	chr1:220991600-221000800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:220992000-221002600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:220992800-221001200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:220993200-221000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:220993200-221001000	Weak transcription	Ovary	ovary
12	chr1:220993400-221001000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:220995000-221001000	Weak transcription	Right Atrium	heart
14	chr1:220995600-221005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:220996000-221001400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:220997400-221003400	Enhancers	Liver	Liver
17	chr1:220998000-221000800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:220998000-221001600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:220998200-221000800	Weak transcription	Spleen	Spleen
20	chr1:220998200-221001600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:220998200-221004200	Weak transcription	Aorta	Aorta
22	chr1:220999200-221000400	Enhancers	Colon Smooth Muscle	Colon
23	chr1:220999200-221002800	Enhancers	Fetal Lung	lung
24	chr1:220999200-221003600	Enhancers	Fetal Heart	heart
25	chr1:220999600-221000400	Enhancers	Fetal Muscle Leg	muscle
26	chr1:220999600-221000600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:220999600-221001800	Enhancers	Lung	lung
28	chr1:220999800-221000400	Enhancers	Right Ventricle	heart
29	chr1:220999800-221000800	Weak transcription	HUVEC	blood vessel
30	chr1:220999800-221001400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:220999800-221002200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:220999800-221002600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:221000000-221000600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr1:221000000-221000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:221000000-221001000	Weak transcription	Left Ventricle	heart
36	chr1:221000000-221001200	Weak transcription	Adipose Nuclei	Adipose
37	chr1:221000000-221001400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:221000000-221002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:221000200-221000400	Enhancers	Placenta	Placenta
40	chr1:221000200-221001200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:221000200-221001800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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