Variant report

Variant	rs6473893
Chromosome Location	chr8:54753508-54753509
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	MAFK	chr8:54753399-54753566	HepG2	liver:	n/a	chr8:54753482-54753496 chr8:54753479-54753494

No.	Distal block	Cell Line	Cell type
1	chr8:54749963..54753631-chr8:54753914..54756219,5	MCF-7	breast:
2	chr8:54733544..54735901-chr8:54752993..54755423,2	MCF-7	breast:
3	chr8:53624816..53627483-chr8:54753343..54757526,4	K562	blood:

Variant related genes	Relation type
ATP6V1H	TF binding region
ENSG00000047249	Chromatin interaction
ENSG00000023287	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1031979	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1031980	1.00[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs10435587	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs12056486	0.88[EUR][1000 genomes]
rs12056719	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs12115070	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12234972	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1552148	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs16919507	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16919508	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs16919522	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16919534	1.00[CEU][hapmap];0.91[MEX][hapmap];0.88[EUR][1000 genomes]
rs16919537	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16919541	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16919563	1.00[CEU][hapmap]
rs16919571	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs16919573	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1872063	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs1905061	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2128150	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2170444	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2376011	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3735831	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs3757954	0.81[EUR][1000 genomes]
rs3824121	0.81[GIH][hapmap]
rs41321146	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4236945	1.00[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs4737192	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4737518	0.81[ASN][1000 genomes]
rs4737554	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs4737558	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs4737753	0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4737761	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4737764	1.00[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs4737765	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.98[EUR][1000 genomes]
rs4737821	1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs4737974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4738025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4738027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4738701	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4738884	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs4738916	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs55682919	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55876329	0.91[EUR][1000 genomes]
rs56818292	0.86[EUR][1000 genomes]
rs56956173	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56973376	0.91[EUR][1000 genomes]
rs57071607	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57550901	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6473894	0.83[ASW][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6984257	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6986372	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs6987427	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6988009	1.00[CEU][hapmap]
rs6988082	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6988808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6988812	0.88[EUR][1000 genomes]
rs6994851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997003	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6997127	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6999454	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7005696	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7006934	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7009705	0.80[ASN][1000 genomes]
rs7018162	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs73680316	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73680321	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73682549	0.91[EUR][1000 genomes]
rs73682551	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73682552	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73682555	0.91[EUR][1000 genomes]
rs73682568	0.95[EUR][1000 genomes]
rs73682570	0.86[EUR][1000 genomes]
rs7843701	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs900163	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs958268	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9643820	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6473893	FZD6	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54687600-54753600	Weak transcription	A549	lung
2	chr8:54710200-54755000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:54714600-54754000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:54724800-54754800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:54735800-54753600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:54738600-54753800	Strong transcription	Fetal Thymus	thymus
7	chr8:54738800-54754800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:54738800-54755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:54741200-54754000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr8:54741600-54753600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:54741600-54753800	Weak transcription	Right Ventricle	heart
12	chr8:54741800-54754800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:54742000-54753600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr8:54742000-54753800	Weak transcription	Colonic Mucosa	Colon
15	chr8:54743200-54753600	Strong transcription	Primary B cells from cord blood	blood
16	chr8:54744200-54753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr8:54744200-54753600	Weak transcription	Fetal Brain Male	brain
18	chr8:54744200-54753600	Weak transcription	NHLF	lung
19	chr8:54744200-54754800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr8:54745600-54753800	Strong transcription	Fetal Stomach	stomach
21	chr8:54745600-54754000	Strong transcription	Fetal Muscle Leg	muscle
22	chr8:54746000-54753600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:54746400-54753600	Weak transcription	K562	blood
24	chr8:54746400-54753600	Weak transcription	Osteobl	bone
25	chr8:54746400-54753800	Weak transcription	Right Atrium	heart
26	chr8:54746400-54753800	Weak transcription	HSMMtube	muscle
27	chr8:54746800-54753600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr8:54748600-54753600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr8:54748800-54753800	Weak transcription	Brain Substantia Nigra	brain
30	chr8:54749400-54753800	Weak transcription	Fetal Lung	lung
31	chr8:54750400-54754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:54750600-54753800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr8:54750600-54755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr8:54750800-54754200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:54751200-54753600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:54751200-54753800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr8:54751400-54753600	Weak transcription	NH-A	brain
38	chr8:54751600-54753600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr8:54751600-54753600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr8:54751600-54753600	Genic enhancers	Dnd41	blood
41	chr8:54751600-54754000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr8:54751600-54754200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr8:54751600-54754400	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr8:54752000-54753600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:54752000-54753600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr8:54752000-54753600	Genic enhancers	NHEK	skin
47	chr8:54752000-54753800	Enhancers	Pancreas	Pancrea
48	chr8:54752000-54754800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr8:54752200-54753600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr8:54752200-54754000	Enhancers	Primary T helper cells fromperipheralblood	blood

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