Variant report

Variant	rs2772469
Chromosome Location	chr3:67603153-67603154
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1122766	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069557	0.81[ASN][1000 genomes]
rs1590874	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1928550	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1928565	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250952	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2634723	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2634732	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634736	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2634737	0.86[AMR][1000 genomes]
rs2634738	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2634740	0.86[AMR][1000 genomes]
rs2634742	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2634743	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2634744	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2772447	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2772448	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2772449	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2772450	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2772451	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2772452	0.83[ASN][1000 genomes]
rs2772453	0.83[ASN][1000 genomes]
rs2772456	0.83[ASN][1000 genomes]
rs2772471	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856788	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9818350	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking 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 target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	9 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	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
2	chr3:67578200-67612400	Weak transcription	Spleen	Spleen
3	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:67579200-67603400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:67579200-67608800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:67579200-67620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:67579400-67623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:67579400-67633800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
10	chr3:67580000-67606400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:67580800-67620200	Weak transcription	GM12878-XiMat	blood
12	chr3:67582200-67637000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:67582400-67609000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:67582400-67620400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:67582600-67612000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:67587000-67620200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:67587400-67628000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:67589800-67615000	Weak transcription	HSMMtube	muscle
19	chr3:67591400-67620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:67591600-67606200	Weak transcription	Liver	Liver
21	chr3:67591600-67611200	Weak transcription	HepG2	liver
22	chr3:67593000-67604600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:67594000-67612400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:67594000-67620600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:67594000-67631000	Weak transcription	K562	blood
26	chr3:67594400-67610400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:67594800-67605200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:67594800-67606200	Weak transcription	Osteobl	bone
29	chr3:67595000-67639400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:67596200-67603400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:67596200-67608200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:67596200-67608800	Weak transcription	Small Intestine	intestine
33	chr3:67596400-67629000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:67598000-67644200	Weak transcription	NHLF	lung
35	chr3:67598200-67618400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:67598800-67616400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:67599600-67604000	Strong transcription	Primary B cells from cord blood	blood
38	chr3:67599600-67604600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:67599600-67620800	Weak transcription	Dnd41	blood
40	chr3:67599600-67621000	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:67599600-67629000	Weak transcription	Right Ventricle	heart
42	chr3:67600000-67603200	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:67600000-67608200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:67600200-67603400	Weak transcription	Thymus	Thymus
45	chr3:67600200-67628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:67600400-67620600	Weak transcription	HMEC	breast
47	chr3:67600400-67624400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:67600600-67611600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:67600800-67621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:67601000-67609800	Strong transcription	Duodenum Mucosa	Duodenum

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