Variant report

Variant	rs1084977
Chromosome Location	chr1:211572519-211572520
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211554866..211557592-chr1:211571886..211574017,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-1	chr1:211572502-211572779	NONHSAT009292

Variant related genes	Relation type
ENSG00000153363	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1084982	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1084983	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1084986	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11804635	0.85[AFR][1000 genomes]
rs12057566	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1533220	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1663521	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1707247	0.82[AMR][1000 genomes]
rs1707252	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1707266	0.80[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1877476	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1983259	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3123302	0.82[AMR][1000 genomes]
rs3855878	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4951735	1.00[TSI][hapmap]
rs6540676	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6661043	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6663627	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6671526	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs784366	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs784370	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs784374	0.93[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs784375	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs784378	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs784380	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs784381	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs784388	0.82[AMR][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	esv3321965	chr1:211571888-211574349	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv3430720	chr1:211571934-211574302	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211556800-211585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:211556800-211589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:211557000-211573200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:211557000-211575000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:211557000-211576600	Weak transcription	Left Ventricle	heart
6	chr1:211557000-211580600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:211557000-211581000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:211557000-211581800	Weak transcription	Fetal Kidney	kidney
9	chr1:211557200-211572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:211557200-211573400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:211557400-211572800	Weak transcription	Fetal Intestine Large	intestine
12	chr1:211557400-211572800	Weak transcription	K562	blood
13	chr1:211557400-211574400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:211557400-211574400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:211557400-211575600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:211557400-211576000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:211557600-211573400	Weak transcription	GM12878-XiMat	blood
18	chr1:211557600-211573400	Weak transcription	Hela-S3	cervix
19	chr1:211557600-211576200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:211561600-211573000	Weak transcription	Right Ventricle	heart
21	chr1:211565200-211573000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:211565600-211574000	Strong transcription	Liver	Liver
23	chr1:211566200-211572800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:211566800-211574600	Weak transcription	Pancreas	Pancrea
25	chr1:211566800-211574800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:211566800-211576800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:211567000-211574600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:211567000-211581600	Weak transcription	Gastric	stomach
29	chr1:211568200-211573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:211568200-211575000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:211568400-211573000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:211568600-211573600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:211569000-211576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:211569600-211572600	Weak transcription	Placenta	Placenta
35	chr1:211569800-211573600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:211570000-211572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:211570000-211573000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:211570000-211573200	Weak transcription	Ovary	ovary
39	chr1:211570000-211574800	Weak transcription	Adipose Nuclei	Adipose
40	chr1:211570000-211575000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:211570200-211574800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:211570800-211581000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:211571600-211573000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:211571600-211573000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:211571600-211573800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr1:211571600-211573800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr1:211571800-211573000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:211571800-211574400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:211572000-211572800	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:211572000-211572800	Active TSS	iPS-18 Cell Line	embryonic stem cell

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