Variant report

Variant	rs12128174
Chromosome Location	chr1:227433256-227433257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10916112	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916113	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10916116	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916125	0.96[AMR][1000 genomes]
rs11576239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11584325	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11585910	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12119153	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12123597	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12131061	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131933	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12133230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138092	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12138364	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138383	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138664	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12144205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12746316	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12754677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755770	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513607	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1513613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17613235	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063661	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28648445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113967	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34702208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35160496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35952573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308948	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61834323	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61834324	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61834590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61834626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6660168	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6678714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7512871	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7518813	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7523759	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539662	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7543419	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7548118	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227414200-227453800	Weak transcription	HSMM	muscle
5	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
7	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:227425400-227445200	Weak transcription	Osteobl	bone
9	chr1:227430600-227433400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:227430600-227434000	Enhancers	Brain Anterior Caudate	brain
11	chr1:227430600-227434000	Enhancers	Pancreas	Pancrea
12	chr1:227430600-227434600	Enhancers	Fetal Heart	heart
13	chr1:227430800-227434200	Enhancers	Gastric	stomach
14	chr1:227431000-227433600	Enhancers	Stomach Smooth Muscle	stomach
15	chr1:227431400-227434000	Enhancers	Brain Hippocampus Middle	brain
16	chr1:227431400-227434200	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:227431600-227435400	Weak transcription	NHLF	lung
18	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
19	chr1:227431800-227439200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:227431800-227443000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:227432000-227433600	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:227432000-227434400	Enhancers	Brain Substantia Nigra	brain
23	chr1:227432000-227434800	Enhancers	HepG2	liver
24	chr1:227432000-227435200	Weak transcription	Fetal Brain Female	brain
25	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
26	chr1:227432200-227434200	Enhancers	Right Atrium	heart
27	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:227432400-227433400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:227432400-227433600	Enhancers	Small Intestine	intestine
30	chr1:227432400-227434000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:227432400-227434000	Weak transcription	Placenta	Placenta
32	chr1:227432400-227434200	Enhancers	Adipose Nuclei	Adipose
33	chr1:227432400-227434200	Enhancers	Left Ventricle	heart
34	chr1:227432400-227434200	Enhancers	Right Ventricle	heart
35	chr1:227432400-227434800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:227432400-227434800	Enhancers	HMEC	breast
37	chr1:227432400-227435000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:227432600-227433400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:227432600-227433800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:227432600-227434000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:227432600-227434000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:227432600-227434200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:227432600-227434200	Enhancers	Lung	lung
44	chr1:227432600-227434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:227432600-227435200	Enhancers	Liver	Liver
46	chr1:227432600-227436200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:227432800-227433400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:227432800-227433400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:227432800-227433600	Weak transcription	Fetal Muscle Trunk	muscle

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