Variant report

Variant	rs12088965
Chromosome Location	chr1:228442865-228442866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10158275	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1188697	0.81[EUR][1000 genomes]
rs12407114	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12727512	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12728259	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12737540	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs287603	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs287604	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs287605	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs287606	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3856331	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391597	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs395285	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs397637	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs424645	0.90[EUR][1000 genomes]
rs438382	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs453140	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs481986	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482888	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs510931	0.90[EUR][1000 genomes]
rs540662	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs549590	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6701173	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7521297	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
16	nsv873268	chr1:228442663-228537942	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv873269	chr1:228442663-228543800	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:228434600-228444400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:228434800-228444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:228434800-228444000	Weak transcription	Ovary	ovary
7	chr1:228434800-228444600	Strong transcription	Dnd41	blood
8	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:228435000-228444000	Weak transcription	Esophagus	oesophagus
12	chr1:228435000-228446000	Weak transcription	A549	lung
13	chr1:228435200-228443200	Weak transcription	Fetal Kidney	kidney
14	chr1:228435200-228449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
16	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:228435800-228446400	Weak transcription	Fetal Heart	heart
19	chr1:228435800-228450200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:228436800-228447000	Weak transcription	Psoas Muscle	Psoas
21	chr1:228437000-228443800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:228437000-228455600	Weak transcription	Hela-S3	cervix
23	chr1:228438000-228443800	Weak transcription	Gastric	stomach
24	chr1:228438000-228444800	Weak transcription	Pancreas	Pancrea
25	chr1:228438200-228443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:228438200-228443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:228438200-228444200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:228438400-228443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:228438400-228447000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:228438400-228455600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:228438600-228443400	Weak transcription	Fetal Lung	lung
32	chr1:228438800-228444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:228439000-228444000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:228439200-228444000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:228439200-228445200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:228439200-228449400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:228439400-228444200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:228439600-228443800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:228439600-228444200	Weak transcription	Spleen	Spleen
40	chr1:228439800-228443000	Weak transcription	Right Ventricle	heart
41	chr1:228439800-228448800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:228440000-228443000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:228440000-228444000	Weak transcription	Lung	lung
44	chr1:228440200-228443200	Weak transcription	Fetal Brain Female	brain
45	chr1:228440200-228443200	Weak transcription	Fetal Intestine Large	intestine
46	chr1:228440200-228443400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:228440200-228443800	Weak transcription	Brain Germinal Matrix	brain
48	chr1:228440200-228444000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:228440200-228444200	Weak transcription	Fetal Thymus	thymus
50	chr1:228440200-228447000	Weak transcription	Right Atrium	heart

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