Variant report

Variant	rs3098254
Chromosome Location	chr8:104405099-104405100
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104402820..104405998-chr8:104409229..104410954,4	MCF-7	breast:
2	chr8:104384922..104387635-chr8:104403443..104406734,3	MCF-7	breast:
3	chr8:104400267..104406502-chr8:104423386..104427069,5	K562	blood:
4	chr8:104403139..104408438-chr8:104419869..104423025,6	K562	blood:
5	chr8:104401208..104405161-chr8:104423386..104426686,3	K562	blood:
6	chr8:104404764..104407750-chr8:104413143..104414836,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164934	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17229709	1.00[MKK][hapmap]
rs17804400	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2575690	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2575695	0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2575700	0.85[GIH][hapmap]
rs2687358	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2687360	0.81[GIH][hapmap]
rs3098228	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]
rs3098229	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3098232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098241	0.82[MEX][hapmap]
rs3098246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098247	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133801	0.97[ASN][1000 genomes]
rs3133803	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs3133805	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3134254	0.82[MEX][hapmap]
rs719842	0.96[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	nsv611832	chr8:104400808-104481735	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	esv2753239	chr8:104404824-104545824	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3098254	DCAF13	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104384400-104412200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr8:104384600-104409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:104384600-104418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:104385000-104408800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr8:104385000-104415600	Weak transcription	Placenta	Placenta
6	chr8:104385600-104405400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:104385600-104408400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:104385600-104423600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:104385600-104424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:104385800-104409000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr8:104385800-104409000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr8:104386000-104409800	Weak transcription	NHLF	lung
13	chr8:104386000-104418600	Weak transcription	Aorta	Aorta
14	chr8:104386000-104425600	Weak transcription	HSMMtube	muscle
15	chr8:104386200-104405600	Weak transcription	HUVEC	blood vessel
16	chr8:104388200-104412200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr8:104393200-104423600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr8:104393600-104409800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr8:104394800-104421800	Weak transcription	Small Intestine	intestine
20	chr8:104397400-104412400	Weak transcription	Brain Hippocampus Middle	brain
21	chr8:104398200-104409200	Weak transcription	Thymus	Thymus
22	chr8:104398600-104413000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr8:104399400-104412200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:104400000-104408600	Weak transcription	Fetal Stomach	stomach
25	chr8:104400000-104426000	Weak transcription	Stomach Mucosa	stomach
26	chr8:104400200-104425600	Weak transcription	Colonic Mucosa	Colon
27	chr8:104400400-104410000	Weak transcription	Psoas Muscle	Psoas
28	chr8:104400600-104410800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr8:104400600-104422400	Weak transcription	Lung	lung
30	chr8:104400800-104405400	Weak transcription	HMEC	breast
31	chr8:104400800-104407400	Weak transcription	Brain Substantia Nigra	brain
32	chr8:104400800-104408000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr8:104400800-104408600	Weak transcription	NHDF-Ad	bronchial
34	chr8:104400800-104409600	Weak transcription	Hela-S3	cervix
35	chr8:104400800-104410600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:104400800-104410800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr8:104400800-104412200	Weak transcription	Fetal Lung	lung
38	chr8:104400800-104412400	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:104400800-104418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr8:104401000-104405200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:104401000-104405600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr8:104401000-104407800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr8:104401000-104408600	Weak transcription	Brain Anterior Caudate	brain
44	chr8:104401000-104408600	Weak transcription	NH-A	brain
45	chr8:104401000-104409200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr8:104401000-104409200	Weak transcription	HSMM	muscle
47	chr8:104401000-104409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr8:104401000-104410000	Weak transcription	Right Ventricle	heart
49	chr8:104401000-104410200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr8:104401000-104411800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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