Variant report

Variant	rs5997621
Chromosome Location	chr22:30754972-30754973
allele	C/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	GATA2	chr22:30754789-30755186	SH-SY5Y	brain:	n/a	chr22:30754989-30755001 chr22:30754990-30755000
2	GATA3	chr22:30754816-30755163	SH-SY5Y	brain:	n/a	chr22:30754989-30755001 chr22:30754990-30754998 chr22:30754990-30755000

No.	Distal block	Cell Line	Cell type
1	chr22:30679588..30687274-chr22:30748772..30756086,11	MCF-7	breast:
2	chr22:30681963..30685470-chr22:30751422..30755510,6	K562	blood:
3	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
4	chr22:30732348..30737677-chr22:30750921..30755238,7	MCF-7	breast:

Variant related genes	Relation type
SF3A1	TF binding region
ENSG00000239282	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000099992	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12157860	1.00[AMR][1000 genomes]
rs57907583	1.00[AMR][1000 genomes]
rs5994294	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs5997635	0.82[AFR][1000 genomes]
rs5997649	0.93[YRI][hapmap]
rs7287885	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs7291572	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881407	1.00[AMR][1000 genomes]
rs73881419	1.00[AMR][1000 genomes]
rs73881429	1.00[AMR][1000 genomes]
rs73881440	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881449	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8137033	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs8142835	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30753200-30782200	Weak transcription	Stomach Mucosa	stomach
2	chr22:30753400-30761600	Weak transcription	Esophagus	oesophagus
3	chr22:30753400-30771400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr22:30753400-30775200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr22:30753400-30776000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr22:30753400-30777000	Weak transcription	Aorta	Aorta
7	chr22:30753600-30755200	Enhancers	Fetal Intestine Large	intestine
8	chr22:30753600-30755400	Weak transcription	Fetal Stomach	stomach
9	chr22:30753600-30758200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:30753600-30758600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:30753600-30758600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:30753600-30761600	Weak transcription	Lung	lung
13	chr22:30753600-30761800	Weak transcription	Fetal Lung	lung
14	chr22:30753600-30762000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr22:30753600-30765800	Weak transcription	Fetal Kidney	kidney
16	chr22:30753600-30765800	Weak transcription	Pancreas	Pancrea
17	chr22:30753600-30766400	Weak transcription	Placenta	Placenta
18	chr22:30753600-30769200	Weak transcription	Brain Hippocampus Middle	brain
19	chr22:30753600-30769400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr22:30753600-30770000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:30753600-30770200	Weak transcription	Brain Substantia Nigra	brain
22	chr22:30753600-30771400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:30753600-30772600	Weak transcription	NHLF	lung
24	chr22:30753600-30772800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:30753600-30773000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr22:30753600-30773000	Weak transcription	Gastric	stomach
27	chr22:30753600-30773400	Weak transcription	Right Ventricle	heart
28	chr22:30753600-30775400	Weak transcription	Colon Smooth Muscle	Colon
29	chr22:30753600-30775400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr22:30753600-30776200	Weak transcription	Thymus	Thymus
31	chr22:30753600-30779200	Weak transcription	Left Ventricle	heart
32	chr22:30753600-30779400	Weak transcription	NHEK	skin
33	chr22:30753600-30779600	Weak transcription	NH-A	brain
34	chr22:30753600-30782000	Weak transcription	Colonic Mucosa	Colon
35	chr22:30753600-30782000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr22:30753600-30782200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr22:30753600-30782400	Weak transcription	Primary T cells from cord blood	blood
38	chr22:30753800-30755600	Enhancers	Fetal Intestine Small	intestine
39	chr22:30753800-30757800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr22:30753800-30768800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr22:30753800-30773400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr22:30753800-30775400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr22:30754000-30761600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr22:30754000-30762000	Weak transcription	Spleen	Spleen
45	chr22:30754000-30768800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr22:30754000-30771400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:30754000-30773400	Weak transcription	Liver	Liver
48	chr22:30754200-30757400	Weak transcription	Fetal Thymus	thymus
49	chr22:30754200-30757800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr22:30754200-30758400	Weak transcription	H1 Cell Line	embryonic stem cell

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