Variant report

Variant	rs419754
Chromosome Location	chr8:90767680-90767681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr8:90767285-90768250	K562	blood:	n/a	n/a
2	POLR2A	chr8:90767584-90768414	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr8:90767659-90767869	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr8:90767223-90768196	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90766999..90771986-chr8:90912842..90916534,13	MCF-7	breast:
2	chr8:90767168..90772413-chr8:90911120..90917480,11	K562	blood:
3	chr8:90766360..90773428-chr8:90991217..91000142,22	MCF-7	breast:
4	chr8:90767236..90773457-chr8:90912212..90919638,16	MCF-7	breast:
5	chr8:90736815..90743993-chr8:90765696..90773918,18	MCF-7	breast:
6	chr8:90753685..90756450-chr8:90766720..90768459,2	MCF-7	breast:
7	chr8:90766719..90773256-chr8:90991979..90999179,19	MCF-7	breast:

No data

Variant related genes	Relation type
RIPK2	TF binding region
ENSG00000164823	Chromatin interaction
ENSG00000207359	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1003843	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10095743	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10112852	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13252013	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13252917	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13259882	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13279023	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs218895	0.81[EUR][1000 genomes]
rs218899	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218900	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs218901	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs218902	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs218905	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs218907	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs218908	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs218909	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs218910	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218913	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs218914	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs218925	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs218929	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs218932	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs218934	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs218936	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs218944	0.81[EUR][1000 genomes]
rs218946	0.82[EUR][1000 genomes]
rs218947	0.82[EUR][1000 genomes]
rs2644021	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644033	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735870	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735871	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735873	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735878	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735882	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs370282	0.86[AMR][1000 genomes]
rs383592	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs385524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394108	0.80[AMR][1000 genomes]
rs39499	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39500	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39503	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39506	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39509	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs39761	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39767	0.80[AMR][1000 genomes]
rs400411	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40246	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs40247	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs402886	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40382	0.85[AMR][1000 genomes]
rs40452	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40453	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40544	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40545	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40547	0.83[AMR][1000 genomes]
rs405734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40636	0.87[AMR][1000 genomes]
rs40638	0.86[AMR][1000 genomes]
rs411279	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs416324	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs42346	0.87[AMR][1000 genomes]
rs42490	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs431264	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs43134	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs43135	0.84[AMR][1000 genomes]
rs43225	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs447618	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs454441	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs465	0.85[AMR][1000 genomes]
rs51331	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6470366	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67143546	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6992985	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6993133	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][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	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs419754	RP11-37B2.1	cis	Artery Tibial	GTEx
rs419754	RP11-37B2.1	cis	Thyroid	GTEx
rs419754	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs419754	RP11-37B2.1	cis	Nerve Tibial	GTEx
rs419754	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90741600-90768200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:90746200-90767800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:90749600-90768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:90749800-90767800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:90749800-90768000	Weak transcription	Left Ventricle	heart
6	chr8:90749800-90768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr8:90750000-90769000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:90756400-90769200	Weak transcription	Pancreas	Pancrea
9	chr8:90758400-90769000	Weak transcription	Ovary	ovary
10	chr8:90760000-90768200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:90760200-90768000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:90760400-90767800	Weak transcription	Fetal Lung	lung
13	chr8:90760600-90768800	Weak transcription	Fetal Kidney	kidney
14	chr8:90760600-90769000	Weak transcription	HSMM	muscle
15	chr8:90762600-90768200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr8:90762600-90768200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr8:90762600-90768800	Weak transcription	Aorta	Aorta
18	chr8:90762600-90769200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:90763000-90768000	Weak transcription	Liver	Liver
20	chr8:90763600-90768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:90764000-90768200	Weak transcription	Placenta	Placenta
22	chr8:90765400-90771600	Active TSS	GM12878-XiMat	blood
23	chr8:90766200-90772400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:90766400-90768000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr8:90766400-90771400	Active TSS	K562	blood
26	chr8:90766600-90768000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr8:90766600-90768000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr8:90766600-90768400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr8:90766600-90771200	Active TSS	NHLF	lung
30	chr8:90766800-90767800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr8:90766800-90768000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr8:90766800-90768000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:90766800-90768000	Enhancers	Hela-S3	cervix
34	chr8:90766800-90768400	Weak transcription	Primary B cells from cord blood	blood
35	chr8:90766800-90769000	Weak transcription	Stomach Mucosa	stomach
36	chr8:90766800-90771800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr8:90767000-90768000	Weak transcription	NHDF-Ad	bronchial
38	chr8:90767000-90768200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr8:90767000-90771200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr8:90767200-90767800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr8:90767400-90767800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr8:90767400-90767800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:90767400-90767800	Active TSS	Osteobl	bone
44	chr8:90767400-90768000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:90767400-90768000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr8:90767400-90768000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr8:90767400-90768200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr8:90767400-90768200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr8:90767400-90768400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr8:90767400-90768600	Enhancers	Cortex derived primary cultured neurospheres	brain

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