Variant report

Variant	rs28690902
Chromosome Location	chr8:19464976-19464977
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr8:19464898-19465224	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA2	chr8:19464684-19465434	SH-SY5Y	brain:	n/a	chr8:19464810-19464819 chr8:19465342-19465354 chr8:19465343-19465353
3	STAT3	chr8:19464900-19465112	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT1	chr8:19464787-19465322	Hela-S3	cervix:	n/a	chr8:19465066-19465077

Variant related genes	Relation type
CSGALNACT1	TF binding region

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1105046	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11993402	0.84[ASN][1000 genomes]
rs13252416	0.86[ASN][1000 genomes]
rs13260856	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13261887	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28558562	0.86[ASN][1000 genomes]
rs34453606	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34632038	0.85[EUR][1000 genomes]
rs35101845	0.80[ASN][1000 genomes]
rs4457347	0.80[ASN][1000 genomes]
rs4472533	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4574860	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636223	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922066	0.84[ASN][1000 genomes]
rs6984585	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6988797	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6988825	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6997538	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7003381	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7828030	0.83[EUR][1000 genomes]
rs9987387	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv890626	chr8:19383697-19483259	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv610754	chr8:19419494-19525294	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv610756	chr8:19434021-19471977	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19445600-19481400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:19456200-19479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:19457600-19465000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:19457600-19472200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr8:19459400-19472000	Weak transcription	Primary T cells from cord blood	blood
6	chr8:19459400-19472200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr8:19460200-19465000	Weak transcription	Adipose Nuclei	Adipose
8	chr8:19460200-19467400	Weak transcription	Spleen	Spleen
9	chr8:19460200-19474200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:19460200-19474200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:19460400-19465000	Weak transcription	Aorta	Aorta
12	chr8:19460400-19465000	Weak transcription	NHLF	lung
13	chr8:19460400-19465600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:19460400-19466200	Weak transcription	Brain Angular Gyrus	brain
15	chr8:19460400-19466600	Enhancers	Fetal Lung	lung
16	chr8:19461000-19465000	Weak transcription	Brain Germinal Matrix	brain
17	chr8:19461000-19465000	Weak transcription	Esophagus	oesophagus
18	chr8:19461000-19465000	Weak transcription	Left Ventricle	heart
19	chr8:19461800-19465600	Weak transcription	Right Atrium	heart
20	chr8:19462000-19465000	Weak transcription	Brain Anterior Caudate	brain
21	chr8:19462200-19465600	Enhancers	Primary B cells from cord blood	blood
22	chr8:19462400-19465200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr8:19462600-19465600	Enhancers	Primary hematopoietic stem cells	blood
24	chr8:19463000-19465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:19463000-19465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:19463000-19465200	Enhancers	A549	lung
27	chr8:19463000-19465400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr8:19463400-19465200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr8:19463400-19473200	Enhancers	Primary B cells from peripheral blood	blood
30	chr8:19464000-19467000	Enhancers	Hela-S3	cervix
31	chr8:19464200-19465200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:19464200-19472200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr8:19464200-19476400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:19464400-19465400	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr8:19464400-19466000	Enhancers	Fetal Muscle Leg	muscle
36	chr8:19464400-19466400	Enhancers	Ovary	ovary
37	chr8:19464600-19465400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr8:19464600-19465800	Enhancers	Brain Cingulate Gyrus	brain
39	chr8:19464600-19466000	Enhancers	Fetal Brain Male	brain
40	chr8:19464600-19466000	Enhancers	Placenta	Placenta
41	chr8:19464600-19466000	Enhancers	Right Ventricle	heart
42	chr8:19464600-19466200	Enhancers	Fetal Stomach	stomach
43	chr8:19464600-19466400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:19464800-19465400	Enhancers	Brain Substantia Nigra	brain
45	chr8:19464800-19465800	Enhancers	Brain Hippocampus Middle	brain
46	chr8:19464800-19466200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr8:19464800-19466600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr8:19464800-19466600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr8:19464800-19466800	Enhancers	Osteobl	bone
50	chr8:19464800-19467000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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