Variant report

Variant	rs12741048
Chromosome Location	chr1:228441373-228441374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10737429	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916292	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10916293	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1188704	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12755546	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1411912	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411915	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1757130	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771455	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1771456	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1771457	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1888680	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1888681	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2150669	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2487384	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795780	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4085473	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs450088	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653932	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426493	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426494	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426495	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426496	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665929	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668967	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6677503	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517088	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517108	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7526808	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7529241	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532144	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7535667	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs878388	0.84[ASN][1000 genomes]
rs947084	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][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:77 , 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	chr1:228433200-228442400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:228434400-228441600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:228434600-228444400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:228434800-228444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:228434800-228444000	Weak transcription	Ovary	ovary
9	chr1:228434800-228444600	Strong transcription	Dnd41	blood
10	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:228435000-228442400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:228435000-228442800	Weak transcription	Aorta	Aorta
15	chr1:228435000-228444000	Weak transcription	Esophagus	oesophagus
16	chr1:228435000-228446000	Weak transcription	A549	lung
17	chr1:228435200-228443200	Weak transcription	Fetal Kidney	kidney
18	chr1:228435200-228449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
20	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:228435400-228441800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:228435800-228446400	Weak transcription	Fetal Heart	heart
24	chr1:228435800-228450200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:228436800-228447000	Weak transcription	Psoas Muscle	Psoas
26	chr1:228437000-228443800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:228437000-228455600	Weak transcription	Hela-S3	cervix
28	chr1:228438000-228441600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:228438000-228443800	Weak transcription	Gastric	stomach
30	chr1:228438000-228444800	Weak transcription	Pancreas	Pancrea
31	chr1:228438200-228443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:228438200-228443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:228438200-228444200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:228438400-228443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:228438400-228447000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:228438400-228455600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:228438600-228443400	Weak transcription	Fetal Lung	lung
38	chr1:228438800-228444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:228439000-228444000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:228439200-228444000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:228439200-228445200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:228439200-228449400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:228439400-228441800	Weak transcription	Primary B cells from cord blood	blood
44	chr1:228439400-228444200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:228439600-228443800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:228439600-228444200	Weak transcription	Spleen	Spleen
47	chr1:228439800-228443000	Weak transcription	Right Ventricle	heart
48	chr1:228439800-228448800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:228440000-228441400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:228440000-228442000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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