Variant report

Variant	rs28620990
Chromosome Location	chr14:24806852-24806853
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	JUND	chr14:24806383-24806979	HepG2	liver:	n/a	chr14:24806821-24806833 chr14:24806822-24806831 chr14:24806824-24806831 chr14:24806820-24806828
2	JUND	chr14:24806686-24806929	HepG2	liver:	n/a	chr14:24806821-24806833 chr14:24806822-24806831 chr14:24806824-24806831 chr14:24806820-24806828
3	JUN	chr14:24806486-24806888	HepG2	liver:	n/a	chr14:24806821-24806833 chr14:24806822-24806831 chr14:24806535-24806548 chr14:24806824-24806831 chr14:24806820-24806828
4	JUND	chr14:24806621-24806913	HepG2	liver:	n/a	chr14:24806821-24806833 chr14:24806822-24806831 chr14:24806824-24806831 chr14:24806820-24806828
5	FOSL2	chr14:24806608-24807037	HepG2	liver:	n/a	chr14:24806821-24806833 chr14:24806822-24806831 chr14:24806824-24806831 chr14:24806820-24806828

No.	Distal block	Cell Line	Cell type
1	chr14:24796718..24800207-chr14:24803965..24807105,3	MCF-7	breast:
2	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
3	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
4	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
5	chr14:24802266..24804821-chr14:24805922..24808045,3	K562	blood:
6	chr14:24805754..24808104-chr14:24833773..24836418,2	MCF-7	breast:

Variant related genes	Relation type
ADCY4	TF binding region
RIPK3	TF binding region
ENSG00000258973	TF binding region
ENSG00000100445	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000139899	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10143642	0.88[AMR][1000 genomes]
rs10146747	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11844732	0.90[EUR][1000 genomes]
rs12323359	0.88[AMR][1000 genomes]
rs28379107	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28453149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28534905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3181247	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212249	0.90[EUR][1000 genomes]
rs3212250	0.90[EUR][1000 genomes]
rs3212251	0.90[EUR][1000 genomes]
rs3212252	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212253	0.90[EUR][1000 genomes]
rs34106261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45537534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56337365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv564060	chr14:24776401-24809795	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28620990	RIPK3	cis	Esophagus Mucosa	GTEx
rs28620990	RIPK3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24804400-24807800	Weak transcription	Pancreas	Pancrea
2	chr14:24804600-24807200	Weak transcription	Right Atrium	heart
3	chr14:24804600-24807400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr14:24804600-24808000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
5	chr14:24804600-24808200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr14:24804800-24807800	Bivalent Enhancer	HepG2	liver
7	chr14:24804800-24808000	Weak transcription	Liver	Liver
8	chr14:24805000-24807400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:24805000-24807800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr14:24805000-24807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:24805000-24807800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:24805000-24808000	Weak transcription	Small Intestine	intestine
13	chr14:24805200-24807000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr14:24805200-24807400	Genic enhancers	Primary B cells from cord blood	blood
15	chr14:24805200-24807400	Weak transcription	Adipose Nuclei	Adipose
16	chr14:24805200-24807600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr14:24805200-24807800	Weak transcription	Right Ventricle	heart
18	chr14:24805400-24807200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:24805400-24807400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:24805400-24807400	Strong transcription	Colonic Mucosa	Colon
21	chr14:24805400-24807400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr14:24805400-24807600	Strong transcription	Primary T cells from cord blood	blood
23	chr14:24805400-24807600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr14:24805400-24808200	Weak transcription	Osteobl	bone
25	chr14:24805400-24808400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:24805600-24807000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr14:24805600-24807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:24805600-24807600	Genic enhancers	Primary monocytes fromperipheralblood	blood
29	chr14:24805600-24807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr14:24805600-24807800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:24805600-24808200	Strong transcription	Fetal Intestine Small	intestine
32	chr14:24805600-24808400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:24805800-24807200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr14:24805800-24807200	Strong transcription	Lung	lung
35	chr14:24805800-24807200	Strong transcription	Spleen	Spleen
36	chr14:24805800-24807800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:24805800-24808000	Weak transcription	HUVEC	blood vessel
38	chr14:24805800-24808000	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr14:24805800-24808200	Weak transcription	NHDF-Ad	bronchial
40	chr14:24806000-24807000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr14:24806000-24807600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr14:24806000-24808000	Weak transcription	Placenta	Placenta
43	chr14:24806200-24807000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr14:24806200-24807000	Strong transcription	Esophagus	oesophagus
45	chr14:24806200-24807000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr14:24806200-24807400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:24806200-24807400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr14:24806200-24807400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:24806200-24807600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr14:24806200-24807800	Strong transcription	Thymus	Thymus

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