Variant report

Variant	rs6775583
Chromosome Location	chr3:142199821-142199822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10935465	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1129393	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925693	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12695761	0.81[EUR][1000 genomes]
rs13061823	0.80[EUR][1000 genomes]
rs13065075	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067795	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13075471	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085998	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13093869	0.82[EUR][1000 genomes]
rs13098343	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2227928	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227930	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28708455	0.81[EUR][1000 genomes]
rs3922730	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4273389	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4441672	0.81[EUR][1000 genomes]
rs4597728	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57177110	0.81[EUR][1000 genomes]
rs6440086	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440087	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440088	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6440089	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440090	0.84[EUR][1000 genomes]
rs6440091	0.81[EUR][1000 genomes]
rs6440092	0.83[EUR][1000 genomes]
rs6440093	0.83[EUR][1000 genomes]
rs6440094	0.83[EUR][1000 genomes]
rs6768093	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770155	0.84[EUR][1000 genomes]
rs6772400	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775718	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6777255	0.80[ASN][1000 genomes]
rs6780250	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782400	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6785675	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791816	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792259	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6799752	0.84[EUR][1000 genomes]
rs7610557	0.84[EUR][1000 genomes]
rs7623524	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7630130	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7634158	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7641330	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647573	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651071	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7652687	0.80[EUR][1000 genomes]
rs9683085	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9808914	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9808943	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816736	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820353	0.80[EUR][1000 genomes]
rs9820770	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825207	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826786	0.81[EUR][1000 genomes]
rs9828178	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846960	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847364	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9855140	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855919	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9869842	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9871402	0.83[EUR][1000 genomes]
rs9876254	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9879995	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
2	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
3	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:142168000-142200000	Weak transcription	Fetal Kidney	kidney
8	chr3:142170600-142203200	Weak transcription	Spleen	Spleen
9	chr3:142177600-142200200	Weak transcription	Hela-S3	cervix
10	chr3:142177800-142200000	Weak transcription	NH-A	brain
11	chr3:142178000-142200000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:142178200-142200000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:142178400-142200000	Weak transcription	HMEC	breast
14	chr3:142178400-142200200	Weak transcription	Fetal Heart	heart
15	chr3:142178600-142200200	Weak transcription	NHDF-Ad	bronchial
16	chr3:142178600-142200200	Weak transcription	NHEK	skin
17	chr3:142178800-142200000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:142178800-142200000	Weak transcription	K562	blood
19	chr3:142183600-142200000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:142185200-142200200	Weak transcription	Osteobl	bone
21	chr3:142186000-142200000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:142186200-142200200	Weak transcription	HSMM	muscle
23	chr3:142186600-142200000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:142192600-142200000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:142192800-142203000	Weak transcription	Pancreas	Pancrea
26	chr3:142193600-142200000	Weak transcription	A549	lung
27	chr3:142197600-142200200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:142198400-142214400	Weak transcription	Stomach Mucosa	stomach
29	chr3:142198800-142203000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:142199000-142200800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr3:142199000-142201600	ZNF genes & repeats	Primary T cells from cord blood	blood
32	chr3:142199000-142202000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
33	chr3:142199000-142202600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:142199000-142203600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:142199200-142200000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:142199200-142200000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:142199200-142200000	ZNF genes & repeats	Lung	lung
38	chr3:142199200-142200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:142199200-142200200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:142199200-142200400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:142199200-142200400	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr3:142199200-142200400	Strong transcription	Right Ventricle	heart
43	chr3:142199200-142201000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:142199200-142201000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:142199200-142201000	ZNF genes & repeats	Fetal Stomach	stomach
46	chr3:142199200-142201000	Strong transcription	Left Ventricle	heart
47	chr3:142199200-142201200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:142199200-142201200	ZNF genes & repeats	Placenta	Placenta
49	chr3:142199200-142201200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:142199200-142201600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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