Variant report

Variant	rs73398412
Chromosome Location	chr6:24845473-24845474
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	BATF	chr6:24845126-24845516	GM12878	blood:	n/a	n/a
2	RUNX3	chr6:24845053-24845535	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:24845072-24845576	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FAM65B	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16889632	0.89[EUR][1000 genomes]
rs34016544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34298086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45619241	0.90[EUR][1000 genomes]
rs58233236	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61733143	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6899341	0.89[EUR][1000 genomes]
rs6917709	0.82[EUR][1000 genomes]
rs6940247	0.89[EUR][1000 genomes]
rs73396489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73396497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73398404	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751675	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9467275	0.89[EUR][1000 genomes]
rs9467329	0.82[EUR][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
3	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:24804800-24858200	Weak transcription	Gastric	stomach
5	chr6:24808800-24845600	Weak transcription	Fetal Stomach	stomach
6	chr6:24817800-24854400	Strong transcription	Primary B cells from cord blood	blood
7	chr6:24817800-24855800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:24818600-24855800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:24818800-24856000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:24830400-24855800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:24832400-24859600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:24833000-24857800	Weak transcription	Brain Angular Gyrus	brain
14	chr6:24834600-24851600	Weak transcription	HSMM	muscle
15	chr6:24836000-24857200	Weak transcription	Fetal Brain Female	brain
16	chr6:24836200-24845800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:24836200-24847600	Weak transcription	Left Ventricle	heart
18	chr6:24837000-24855800	Weak transcription	Ovary	ovary
19	chr6:24837800-24848400	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr6:24837800-24850000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:24837800-24856000	Strong transcription	Fetal Thymus	thymus
22	chr6:24838000-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:24838200-24854800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr6:24838200-24856000	Strong transcription	Placenta	Placenta
25	chr6:24838200-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:24838400-24849000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:24838400-24851800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr6:24838800-24855800	Weak transcription	Adipose Nuclei	Adipose
29	chr6:24839000-24854800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:24839200-24845600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:24839200-24846000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:24839200-24846400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:24839200-24853600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr6:24839600-24846200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:24839600-24858800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:24840400-24854600	Strong transcription	HSMMtube	muscle
37	chr6:24840400-24854800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:24840400-24854800	Strong transcription	Thymus	Thymus
39	chr6:24840400-24856400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:24840600-24847600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:24840600-24855000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:24841000-24855000	Weak transcription	Colonic Mucosa	Colon
43	chr6:24841200-24854400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:24841200-24854800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr6:24841600-24853400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:24842000-24854800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:24842400-24856600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:24843000-24856000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:24843200-24847600	Weak transcription	Brain Germinal Matrix	brain
50	chr6:24843400-24855800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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