Variant report

Variant	rs1564176
Chromosome Location	chr3:42814602-42814603
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42812718..42815694-chr3:42844363..42847706,3	K562	blood:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11129971	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35426298	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5027058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778695	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.93[AFR][1000 genomes]
rs7648688	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42813000-42821400	Weak transcription	Dnd41	blood
2	chr3:42813000-42821800	Weak transcription	HepG2	liver
3	chr3:42813800-42814800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:42813800-42815200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:42814000-42814800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:42814000-42814800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:42814000-42814800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr3:42814000-42815000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:42814000-42815000	Active TSS	Brain Substantia Nigra	brain
10	chr3:42814000-42815000	Active TSS	Colon Smooth Muscle	Colon
11	chr3:42814000-42815200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:42814000-42815200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:42814000-42815200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:42814000-42815200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr3:42814000-42815200	Active TSS	Brain Angular Gyrus	brain
16	chr3:42814000-42815200	Active TSS	Brain Hippocampus Middle	brain
17	chr3:42814000-42815200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:42814000-42815200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:42814200-42814800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr3:42814200-42814800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:42814200-42814800	Flanking Active TSS	Colonic Mucosa	Colon
22	chr3:42814200-42814800	Flanking Active TSS	Pancreas	Pancrea
23	chr3:42814200-42814800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr3:42814200-42815000	Active TSS	Primary T cells from cord blood	blood
25	chr3:42814200-42815000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:42814200-42815000	Active TSS	Fetal Kidney	kidney
27	chr3:42814200-42815000	Active TSS	NHEK	skin
28	chr3:42814200-42815200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:42814200-42815200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:42814200-42815200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:42814200-42815200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:42814200-42815200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr3:42814200-42815200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr3:42814200-42815200	Active TSS	Fetal Brain Female	brain
35	chr3:42814200-42815200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr3:42814200-42815200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr3:42814200-42815200	Active TSS	Ovary	ovary
38	chr3:42814200-42815200	Active TSS	Right Atrium	heart
39	chr3:42814200-42815200	Flanking Active TSS	HMEC	breast
40	chr3:42814200-42815200	Active TSS	HSMM	muscle
41	chr3:42814200-42815400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:42814200-42815400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:42814200-42815400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr3:42814200-42815400	Active TSS	NHLF	lung
45	chr3:42814400-42814800	Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr3:42814400-42814800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:42814400-42814800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr3:42814400-42815000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:42814400-42815000	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:42814400-42815000	Active TSS	iPS-18 Cell Line	embryonic stem cell

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