Variant report

Variant	rs4549789
Chromosome Location	chr8:19284015-19284016
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	chr8:19283299..19285964-chr8:19292652..19294945,2	MCF-7	breast:
2	chr8:19279205..19280725-chr8:19282957..19284991,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10107416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204039	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204040	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204041	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11780343	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11780388	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11782540	0.83[AMR][1000 genomes]
rs11784873	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11785649	0.83[AMR][1000 genomes]
rs11786847	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11787230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11991105	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12542575	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12543061	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674938	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12675717	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12678336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679671	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12679712	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13255677	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13255946	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13258090	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13278459	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17407039	0.83[AMR][1000 genomes]
rs17407149	0.81[AFR][1000 genomes]
rs17479099	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34156560	0.83[ASN][1000 genomes]
rs35029660	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3802328	0.88[ASN][1000 genomes]
rs4307360	0.81[ASN][1000 genomes]
rs4333618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379462	0.81[EUR][1000 genomes]
rs4391454	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4392915	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4392916	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4409408	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4412390	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4430112	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4431609	0.86[AFR][1000 genomes]
rs4433156	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481612	1.00[ASN][1000 genomes]
rs4546679	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617172	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4618712	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4633071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4921638	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4921642	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4921643	0.88[ASN][1000 genomes]
rs4921645	0.81[ASN][1000 genomes]
rs4922028	0.83[ASN][1000 genomes]
rs6586830	0.88[ASN][1000 genomes]
rs6981898	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6983973	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6984145	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6990217	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6990357	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6991212	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6992893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6997164	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6999786	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7004435	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006702	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7008916	0.87[ASN][1000 genomes]
rs7011602	0.83[EUR][1000 genomes]
rs7012529	0.88[ASN][1000 genomes]
rs7015440	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7016259	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7016592	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7818345	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7820698	0.90[ASN][1000 genomes]
rs7821446	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7822046	0.88[ASN][1000 genomes]
rs7823194	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7833166	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7835461	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7835945	0.90[ASN][1000 genomes]
rs7844175	0.88[ASN][1000 genomes]
rs9720249	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
8	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv610751	chr8:19226335-19284889	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv610752	chr8:19254816-19311496	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
14	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4549789	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx
rs4549789	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19267200-19297000	Weak transcription	Brain Substantia Nigra	brain
2	chr8:19267800-19295600	Weak transcription	Brain Hippocampus Middle	brain
3	chr8:19270200-19288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:19271000-19284200	Weak transcription	Thymus	Thymus
5	chr8:19271800-19305200	Weak transcription	Pancreas	Pancrea
6	chr8:19275800-19287200	Weak transcription	Gastric	stomach
7	chr8:19275800-19288600	Weak transcription	Aorta	Aorta
8	chr8:19275800-19295600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr8:19277600-19295600	Weak transcription	Hela-S3	cervix
10	chr8:19277600-19307800	Weak transcription	Fetal Stomach	stomach
11	chr8:19277800-19300200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr8:19278000-19304800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:19279600-19290600	Weak transcription	Primary B cells from cord blood	blood
14	chr8:19280800-19284800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr8:19280800-19285000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr8:19281000-19285000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr8:19281000-19285000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr8:19281800-19296800	Weak transcription	Lung	lung
19	chr8:19282400-19284400	Enhancers	Primary T cells from cord blood	blood
20	chr8:19282400-19286400	Weak transcription	Esophagus	oesophagus
21	chr8:19282400-19292200	Weak transcription	Fetal Brain Male	brain
22	chr8:19282400-19294800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:19282800-19287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:19283200-19284800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:19283400-19284400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:19283400-19284600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:19283400-19284800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr8:19283600-19284200	Enhancers	Primary hematopoietic stem cells	blood
29	chr8:19283600-19284400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr8:19283600-19284400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr8:19283600-19284400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr8:19283600-19284600	Enhancers	A549	lung
33	chr8:19283600-19284800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr8:19283800-19284200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:19283800-19284400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:19283800-19284800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr8:19283800-19285200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:19283800-19285200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:19283800-19290800	Weak transcription	Placenta	Placenta
40	chr8:19283800-19294800	Weak transcription	Left Ventricle	heart
41	chr8:19283800-19302200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr8:19283800-19307800	Weak transcription	Ovary	ovary
43	chr8:19284000-19287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr8:19284000-19302400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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