Variant report

Variant	rs12727512
Chromosome Location	chr1:228435855-228435856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10158275	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1150906	0.81[EUR][1000 genomes]
rs1188697	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12088965	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12407114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12728259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12737540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs287603	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs287604	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs287605	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs287606	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856331	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs391597	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395285	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407918	0.81[EUR][1000 genomes]
rs412716	0.80[EUR][1000 genomes]
rs424645	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs437129	0.81[EUR][1000 genomes]
rs438382	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447902	0.81[EUR][1000 genomes]
rs453140	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs481986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs482888	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs510931	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540662	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549590	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6701173	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521297	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:228428400-228436600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
3	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle
4	chr1:228430400-228436600	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:228430800-228440000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:228431000-228436000	Strong transcription	Right Ventricle	heart
8	chr1:228431200-228439800	Strong transcription	Left Ventricle	heart
9	chr1:228431400-228436000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:228432000-228436800	Strong transcription	Psoas Muscle	Psoas
11	chr1:228433200-228442400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:228433400-228436400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
14	chr1:228433600-228438000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:228433600-228438400	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr1:228434000-228439600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:228434200-228436600	Strong transcription	Primary B cells from cord blood	blood
18	chr1:228434200-228438600	Strong transcription	Fetal Lung	lung
19	chr1:228434400-228437000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:228434400-228437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:228434400-228440200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:228434400-228440400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:228434400-228441600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:228434600-228437200	Strong transcription	Fetal Intestine Large	intestine
25	chr1:228434600-228437200	Weak transcription	Spleen	Spleen
26	chr1:228434600-228439800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:228434600-228439800	Weak transcription	Right Atrium	heart
28	chr1:228434600-228440200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:228434600-228440200	Strong transcription	Fetal Thymus	thymus
30	chr1:228434600-228440600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:228434600-228444400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:228434800-228436200	Weak transcription	Hela-S3	cervix
34	chr1:228434800-228437200	Weak transcription	Gastric	stomach
35	chr1:228434800-228437400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:228434800-228438400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:228434800-228439200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:228434800-228440600	Strong transcription	Fetal Stomach	stomach
39	chr1:228434800-228444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:228434800-228444000	Weak transcription	Ovary	ovary
41	chr1:228434800-228444600	Strong transcription	Dnd41	blood
42	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:228435000-228436400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:228435000-228436400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:228435000-228437200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:228435000-228437200	Weak transcription	Lung	lung
49	chr1:228435000-228437400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:228435000-228440400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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