Variant report

Variant	rs3098228
Chromosome Location	chr8:104392971-104392972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:104392950-104393059	ProgFib	skin:	n/a	n/a
2	POLR2A	chr8:104392894-104393215	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr8:104392862-104393079	MCF-7	breast:	n/a	n/a
4	POLR2A	chr8:104392867-104393027	HepG2	liver:	n/a	n/a
5	POLR2A	chr8:104391877-104393315	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr8:104392893-104392990	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr8:104310391..104312024-chr8:104392182..104394421,2	MCF-7	breast:
2	chr8:104383459..104385049-chr8:104392946..104395233,2	MCF-7	breast:
3	chr8:104382407..104388323-chr8:104390261..104395573,7	MCF-7	breast:
4	chr8:104388643..104390746-chr8:104392286..104395011,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-1011P	TF binding region
ENSG00000164932	Chromatin interaction
ENSG00000164930	Chromatin interaction
ENSG00000247081	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17804400	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2575690	0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2575695	0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2575700	0.85[GIH][hapmap]
rs2687358	0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2687360	0.81[GIH][hapmap]
rs3098229	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3098230	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3098232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098246	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133801	0.94[ASN][1000 genomes]
rs3133803	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[ASN][1000 genomes]
rs3133805	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3133810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133839	0.81[AMR][1000 genomes]
rs3134293	1.00[YRI][hapmap]
rs719841	0.81[AMR][1000 genomes]
rs719842	0.96[GIH][hapmap];0.92[TSI][hapmap]
rs73699799	0.85[AFR][1000 genomes]
rs750606	0.82[ASW][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1016395	chr8:104327541-104473005	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic 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	29 gene(s)	inside rSNPs	diseases
5	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1021345	chr8:104361854-104879684	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv1032085	chr8:104362187-104878345	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1033477	chr8:104369940-104439632	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv539706	chr8:104369940-104439632	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1034183	chr8:104369940-104814008	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv539707	chr8:104369940-104814008	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3098228	DCAF13	cis	Muscle Skeletal	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104384200-104394800	Weak transcription	GM12878-XiMat	blood
2	chr8:104384200-104399800	Weak transcription	Primary T cells from cord blood	blood
3	chr8:104384400-104412200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:104384600-104409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:104384600-104418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:104385000-104399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:104385000-104408800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr8:104385000-104415600	Weak transcription	Placenta	Placenta
9	chr8:104385400-104400400	Weak transcription	A549	lung
10	chr8:104385600-104399200	Weak transcription	Fetal Stomach	stomach
11	chr8:104385600-104399800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:104385600-104400200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:104385600-104400200	Weak transcription	Fetal Thymus	thymus
14	chr8:104385600-104400600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr8:104385600-104405400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr8:104385600-104408400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr8:104385600-104423600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:104385600-104424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr8:104385800-104393400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr8:104385800-104399800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr8:104385800-104409000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr8:104385800-104409000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr8:104386000-104395600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr8:104386000-104399800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:104386000-104399800	Weak transcription	Fetal Muscle Leg	muscle
26	chr8:104386000-104400200	Weak transcription	Dnd41	blood
27	chr8:104386000-104400600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr8:104386000-104409800	Weak transcription	NHLF	lung
29	chr8:104386000-104418600	Weak transcription	Aorta	Aorta
30	chr8:104386000-104425600	Weak transcription	HSMMtube	muscle
31	chr8:104386200-104405600	Weak transcription	HUVEC	blood vessel
32	chr8:104387000-104399800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:104388200-104412200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr8:104388800-104393200	Strong transcription	Osteobl	bone
35	chr8:104388800-104393800	Strong transcription	NH-A	brain
36	chr8:104389000-104399200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:104389000-104399800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:104389000-104400400	Weak transcription	NHDF-Ad	bronchial
39	chr8:104389400-104395000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:104389400-104396600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:104392000-104393200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:104392000-104393200	Strong transcription	HSMM	muscle
43	chr8:104392000-104395200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:104392600-104393200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr8:104392800-104393000	Enhancers	Psoas Muscle	Psoas
46	chr8:104392800-104393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr8:104392800-104393200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr8:104392800-104393200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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