Variant report

Variant	rs4630978
Chromosome Location	chr3:46150720-46150721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46148560..46157677-chr3:46203034..46208483,12	MCF-7	breast:
2	chr3:46145999..46148966-chr3:46149561..46152328,4	K562	blood:
3	chr3:46145905..46148811-chr3:46150645..46152455,3	MCF-7	breast:
4	chr3:46145999..46148622-chr3:46149561..46152053,3	K562	blood:
5	chr3:46130825..46132979-chr3:46149857..46153032,4	MCF-7	breast:
6	chr3:46149777..46152755-chr3:46160739..46163366,2	MCF-7	breast:
7	chr3:46149539..46152315-chr3:46168852..46171063,2	K562	blood:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10049103	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1078355	0.84[AMR][1000 genomes]
rs12107160	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107288	1.00[EUR][1000 genomes]
rs13325425	1.00[EUR][1000 genomes]
rs1352880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1491954	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1846618	1.00[EUR][1000 genomes]
rs1873615	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2036294	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2036296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2088691	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28393246	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28454181	1.00[EUR][1000 genomes]
rs55743140	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56071453	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56738797	0.84[AMR][1000 genomes]
rs57375372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57590663	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57768435	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57800045	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57887195	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58139750	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58402224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58969771	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59065510	1.00[EUR][1000 genomes]
rs59157393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59676542	1.00[EUR][1000 genomes]
rs59754516	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60080146	0.84[AMR][1000 genomes]
rs61201782	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61276379	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61598729	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61686943	1.00[EUR][1000 genomes]
rs6788758	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791693	0.80[AFR][1000 genomes]
rs6798934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72885402	0.84[AMR][1000 genomes]
rs72887108	0.84[AMR][1000 genomes]
rs72887131	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72887154	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72889737	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72889749	0.85[AFR][1000 genomes]
rs72889759	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72891111	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72891128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72891129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72899100	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904134	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830713	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833519	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7427033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs978316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs978317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9830945	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844424	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852295	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854654	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859291	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9871934	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9882976	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46129400-46154200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:46131400-46152200	Weak transcription	Pancreas	Pancrea
3	chr3:46143800-46153000	Enhancers	Fetal Thymus	thymus
4	chr3:46145200-46152400	Enhancers	Dnd41	blood
5	chr3:46146800-46164400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:46147400-46150800	Weak transcription	Esophagus	oesophagus
7	chr3:46147600-46151400	Enhancers	Thymus	Thymus
8	chr3:46148200-46152800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:46148400-46160200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:46148600-46152800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:46148800-46151400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:46148800-46152800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:46149000-46151200	Enhancers	Small Intestine	intestine
14	chr3:46149000-46151600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:46149000-46152000	Enhancers	GM12878-XiMat	blood
16	chr3:46149000-46152000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr3:46149200-46151400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:46149200-46158800	Enhancers	NHLF	lung
19	chr3:46149200-46159800	Enhancers	Placenta	Placenta
20	chr3:46149400-46151400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:46149400-46152800	Enhancers	HSMM	muscle
22	chr3:46149600-46150800	Enhancers	HSMMtube	muscle
23	chr3:46149600-46151400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:46149600-46151400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:46149600-46152600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:46149800-46151000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:46150000-46151000	Enhancers	Brain Germinal Matrix	brain
28	chr3:46150000-46151200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:46150000-46151200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:46150000-46151200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:46150000-46151200	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:46150000-46151200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:46150000-46151600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr3:46150000-46151600	Enhancers	NHEK	skin
35	chr3:46150000-46152400	Enhancers	Hela-S3	cervix
36	chr3:46150000-46153000	Enhancers	Fetal Lung	lung
37	chr3:46150000-46157600	Enhancers	HMEC	breast
38	chr3:46150200-46150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:46150200-46151200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr3:46150200-46151200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:46150200-46152200	Weak transcription	Fetal Stomach	stomach
42	chr3:46150200-46152400	Enhancers	Primary B cells from cord blood	blood
43	chr3:46150200-46152600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:46150400-46151000	Enhancers	Spleen	Spleen
45	chr3:46150400-46151200	Enhancers	Primary B cells from peripheral blood	blood
46	chr3:46150400-46151400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:46150400-46151400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:46150400-46151400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:46150400-46151600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:46150400-46151600	Enhancers	NH-A	brain

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