Variant report

Variant	rs1877476
Chromosome Location	chr1:211590892-211590893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10732682	0.96[EUR][1000 genomes]
rs10746434	0.86[EUR][1000 genomes]
rs10779554	0.96[EUR][1000 genomes]
rs1084977	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1084982	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1084983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1084986	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10863886	0.96[EUR][1000 genomes]
rs10863887	0.96[EUR][1000 genomes]
rs11804635	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1533219	0.92[EUR][1000 genomes]
rs1533220	0.96[EUR][1000 genomes]
rs1663521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1707247	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1707252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1707266	0.96[EUR][1000 genomes]
rs1707267	0.96[EUR][1000 genomes]
rs1983259	0.96[EUR][1000 genomes]
rs1983260	0.89[EUR][1000 genomes]
rs2358215	0.92[EUR][1000 genomes]
rs2588658	0.88[EUR][1000 genomes]
rs2995846	0.96[EUR][1000 genomes]
rs3123302	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3125840	0.88[EUR][1000 genomes]
rs3855878	0.96[EUR][1000 genomes]
rs4281373	0.83[EUR][1000 genomes]
rs4347268	0.96[EUR][1000 genomes]
rs4370817	0.96[EUR][1000 genomes]
rs4556425	0.96[EUR][1000 genomes]
rs4951517	0.96[EUR][1000 genomes]
rs4951735	0.96[EUR][1000 genomes]
rs4951737	0.96[EUR][1000 genomes]
rs4951738	0.92[EUR][1000 genomes]
rs4951739	0.96[EUR][1000 genomes]
rs4951740	0.92[EUR][1000 genomes]
rs6540675	0.96[EUR][1000 genomes]
rs6540676	0.96[EUR][1000 genomes]
rs6540678	0.96[EUR][1000 genomes]
rs6657779	0.89[EUR][1000 genomes]
rs6663627	0.96[EUR][1000 genomes]
rs6671526	0.96[EUR][1000 genomes]
rs6672233	0.96[EUR][1000 genomes]
rs6688682	0.96[EUR][1000 genomes]
rs6692815	0.96[EUR][1000 genomes]
rs73072839	0.88[EUR][1000 genomes]
rs7517135	0.96[EUR][1000 genomes]
rs7527620	0.96[EUR][1000 genomes]
rs784366	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs784367	0.92[EUR][1000 genomes]
rs784368	0.92[EUR][1000 genomes]
rs784370	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784371	0.85[EUR][1000 genomes]
rs784373	0.92[EUR][1000 genomes]
rs784374	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs784375	1.00[EUR][1000 genomes]
rs784378	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784380	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784387	0.96[EUR][1000 genomes]
rs784388	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
3	esv3362349	chr1:211588754-211591702	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3433824	chr1:211589079-211591127	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211581400-211608200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:211585400-211593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:211589400-211591000	Active TSS	Brain Hippocampus Middle	brain
4	chr1:211589600-211608800	Weak transcription	GM12878-XiMat	blood
5	chr1:211590200-211591000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:211590200-211593600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:211590200-211601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:211590400-211591000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:211590400-211591000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr1:211590400-211591000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:211590400-211591000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:211590400-211591000	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:211590400-211591000	Enhancers	Right Ventricle	heart
14	chr1:211590400-211591000	Enhancers	HMEC	breast
15	chr1:211590400-211591000	Enhancers	NHEK	skin
16	chr1:211590400-211591200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:211590400-211591200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:211590400-211591200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:211590400-211591200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:211590400-211591400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:211590400-211592200	Weak transcription	Spleen	Spleen
22	chr1:211590400-211592600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:211590400-211593600	Weak transcription	Hela-S3	cervix
24	chr1:211590400-211593600	Weak transcription	HSMM	muscle
25	chr1:211590400-211593800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:211590400-211604400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:211590400-211607200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:211590400-211607600	Weak transcription	Left Ventricle	heart
29	chr1:211590400-211609000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:211590600-211591000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:211590600-211591000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:211590600-211591000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:211590600-211591000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:211590600-211591000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:211590600-211591000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:211590600-211591000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:211590600-211591000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:211590600-211591000	Enhancers	NH-A	brain
39	chr1:211590600-211591000	Enhancers	NHLF	lung
40	chr1:211590600-211591200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr1:211590600-211591200	Enhancers	Osteobl	bone
42	chr1:211590600-211591800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:211590600-211591800	Weak transcription	Pancreas	Pancrea
44	chr1:211590600-211593600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:211590600-211602400	Weak transcription	Liver	Liver
46	chr1:211590600-211605600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:211590800-211591000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr1:211590800-211591000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:211590800-211591000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:211590800-211591000	Enhancers	Rectal Mucosa Donor 31	rectum

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