Variant report

Variant	rs11985002
Chromosome Location	chr8:104386138-104386139
allele	A/G
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	SMC3	chr8:104383479-104386604	SK-N-SH	brain:	n/a	chr8:104385611-104385621 chr8:104385611-104385625 chr8:104384498-104384505 chr8:104385618-104385625
2	GATA3	chr8:104384069-104386185	SK-N-SH	brain:	n/a	chr8:104384574-104384583
3	CTCF	chr8:104386000-104386150	NHDF-neo	bronchial:	n/a	n/a
4	CTCF	chr8:104385054-104386172	SK-N-SH	brain:	n/a	chr8:104385609-104385627 chr8:104385615-104385624 chr8:104385612-104385622 chr8:104385604-104385625 chr8:104385611-104385624 chr8:104385610-104385626
5	CTCF	chr8:104386020-104386170	NHDF-neo	bronchial:	n/a	n/a
6	MXI1	chr8:104383388-104386158	IMR90	lung:	n/a	chr8:104383466-104383475 chr8:104383468-104383477
7	POLR2A	chr8:104383342-104386187	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:104384537..104387363-chr8:104425771..104427328,2	MCF-7	breast:
2	chr8:104289531..104293502-chr8:104385386..104388063,3	MCF-7	breast:
3	chr8:104383486..104387596-chr8:104393672..104397600,4	K562	blood:
4	chr8:104385225..104386793-chr8:104395425..104397023,2	K562	blood:
5	chr8:104164158..104164912-chr8:104385376..104386427,3	MCF-7	breast:
6	chr8:104384521..104386453-chr8:104425627..104427344,2	K562	blood:
7	chr8:104309966..104312210-chr8:104383451..104386900,3	MCF-7	breast:
8	chr8:104116271..104117073-chr8:104385047..104386147,6	MCF-7	breast:
9	chr8:104313517..104316996-chr8:104385407..104388642,4	MCF-7	breast:
10	chr8:104382288..104384118-chr8:104384150..104386828,2	MCF-7	breast:
11	chr8:104384840..104386401-chr8:104401334..104403233,2	K562	blood:
12	chr8:104384672..104387548-chr8:104409163..104411650,2	K562	blood:
13	chr8:104384922..104387635-chr8:104403443..104406734,3	MCF-7	breast:

Variant related genes	Relation type
CTHRC1	TF binding region
ENSG00000266289	Chromatin interaction
ENSG00000164930	Chromatin interaction
ENSG00000164934	Chromatin interaction
ENSG00000247081	Chromatin interaction
ENSG00000207399	Chromatin interaction
ENSG00000164932	Chromatin interaction
ENSG00000164933	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10089343	0.83[ASN][1000 genomes]
rs10090069	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094939	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10096207	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097121	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10101517	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102413	0.83[ASN][1000 genomes]
rs10105195	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10105450	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106795	0.83[ASN][1000 genomes]
rs10108112	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10109642	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10112317	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10112450	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10112941	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10112952	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113160	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113367	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061196	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11779349	0.83[ASN][1000 genomes]
rs11785583	0.83[ASN][1000 genomes]
rs12707777	0.83[ASN][1000 genomes]
rs13255562	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13257958	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13258345	0.83[ASN][1000 genomes]
rs13263611	0.83[ASN][1000 genomes]
rs13266347	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266642	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273192	0.83[ASN][1000 genomes]
rs13278335	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13282967	0.83[ASN][1000 genomes]
rs1370007	0.83[AMR][1000 genomes]
rs17205821	0.83[ASN][1000 genomes]
rs17228538	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17802416	0.98[EUR][1000 genomes]
rs17802518	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17804088	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17804149	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28437723	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28811720	1.00[ASN][1000 genomes]
rs28862349	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2948449	0.83[ASN][1000 genomes]
rs3104026	0.83[ASN][1000 genomes]
rs34208282	0.83[ASN][1000 genomes]
rs35225263	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35392014	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57237927	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468866	0.83[ASN][1000 genomes]
rs6985718	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6989714	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990501	0.83[ASN][1000 genomes]
rs71520811	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72675443	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72675444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72675445	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7464317	0.83[ASN][1000 genomes]
rs7820626	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7839421	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845210	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs827528	0.83[ASN][1000 genomes]
rs827537	0.83[ASN][1000 genomes]
rs827538	0.83[ASN][1000 genomes]
rs827546	0.83[ASN][1000 genomes]
rs951826	0.83[ASN][1000 genomes]
rs973242	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs981816	0.83[AMR][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
rs11985002	FZD6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104383400-104386400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr8:104383400-104386600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:104384200-104386400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:104384200-104394800	Weak transcription	GM12878-XiMat	blood
5	chr8:104384200-104399800	Weak transcription	Primary T cells from cord blood	blood
6	chr8:104384400-104388000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:104384400-104388000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:104384400-104412200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr8:104384600-104409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:104384600-104418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:104384800-104387400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:104384800-104392600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr8:104385000-104387000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:104385000-104399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:104385000-104408800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr8:104385000-104415600	Weak transcription	Placenta	Placenta
17	chr8:104385200-104386200	Enhancers	NHEK	skin
18	chr8:104385400-104386800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:104385400-104388400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:104385400-104400400	Weak transcription	A549	lung
21	chr8:104385600-104386200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr8:104385600-104386800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr8:104385600-104387200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:104385600-104389600	Weak transcription	Fetal Brain Male	brain
25	chr8:104385600-104399200	Weak transcription	Fetal Stomach	stomach
26	chr8:104385600-104399800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:104385600-104400200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:104385600-104400200	Weak transcription	Fetal Thymus	thymus
29	chr8:104385600-104400600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr8:104385600-104405400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr8:104385600-104408400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:104385600-104423600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:104385600-104424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr8:104385800-104387000	Transcr. at gene 5' and 3'	NH-A	brain
35	chr8:104385800-104393400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:104385800-104399800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr8:104385800-104409000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr8:104385800-104409000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr8:104386000-104386200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:104386000-104386200	Enhancers	HUVEC	blood vessel
41	chr8:104386000-104386600	Enhancers	Osteobl	bone
42	chr8:104386000-104387200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr8:104386000-104387200	Weak transcription	NHDF-Ad	bronchial
44	chr8:104386000-104387600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:104386000-104388000	Weak transcription	HMEC	breast
46	chr8:104386000-104389000	Weak transcription	HSMM	muscle
47	chr8:104386000-104395600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:104386000-104399800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr8:104386000-104399800	Weak transcription	Fetal Muscle Leg	muscle
50	chr8:104386000-104400200	Weak transcription	Dnd41	blood

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