Variant report

Variant	rs1075262
Chromosome Location	chr6:71117655-71117656
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	MAZ	chr6:71117642-71117797	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:71115718-71119707	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71117346..71119086-chr6:71119610..71121157,2	MCF-7	breast:
2	chr6:71115111..71117977-chr6:71121275..71123919,2	MCF-7	breast:

Variant related genes	Relation type
FAM135A	TF binding region
ENSG00000082269	Chromatin interaction
ENSG00000224349	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10485118	1.00[JPT][hapmap]
rs10485119	1.00[JPT][hapmap]
rs1048886	0.92[JPT][hapmap]
rs1075263	1.00[JPT][hapmap]
rs10945230	1.00[JPT][hapmap]
rs11965656	1.00[JPT][hapmap]
rs1208476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1208477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190556	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs12197942	1.00[JPT][hapmap]
rs12197963	1.00[JPT][hapmap]
rs12203298	1.00[JPT][hapmap]
rs12209965	1.00[JPT][hapmap]
rs12216376	1.00[JPT][hapmap]
rs12526164	1.00[JPT][hapmap]
rs12526827	1.00[JPT][hapmap]
rs12527634	1.00[JPT][hapmap]
rs12529284	1.00[JPT][hapmap]
rs13202450	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13206086	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16869156	1.00[JPT][hapmap]
rs16869158	1.00[JPT][hapmap]
rs16869170	1.00[JPT][hapmap]
rs16869211	0.92[JPT][hapmap]
rs16869221	1.00[JPT][hapmap]
rs16869228	1.00[JPT][hapmap]
rs16869238	1.00[JPT][hapmap]
rs16869243	1.00[JPT][hapmap]
rs16869244	0.92[JPT][hapmap]
rs16869267	1.00[JPT][hapmap]
rs16869273	1.00[JPT][hapmap]
rs16869338	1.00[JPT][hapmap]
rs16869353	1.00[JPT][hapmap]
rs16869370	1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs16869371	1.00[JPT][hapmap]
rs16869373	1.00[JPT][hapmap]
rs16880770	1.00[JPT][hapmap]
rs1739338	1.00[JPT][hapmap]
rs1775338	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207423	1.00[JPT][hapmap]
rs2273210	1.00[JPT][hapmap]
rs2293297	1.00[JPT][hapmap]
rs2295200	1.00[JPT][hapmap]
rs2346889	1.00[JPT][hapmap]
rs2346890	1.00[JPT][hapmap]
rs2347427	0.96[CEU][hapmap]
rs2639297	1.00[JPT][hapmap]
rs2747702	1.00[JPT][hapmap]
rs2747703	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842063	0.92[JPT][hapmap]
rs3193656	1.00[JPT][hapmap]
rs34873840	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35516318	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736751	1.00[JPT][hapmap]
rs3736752	0.92[JPT][hapmap]
rs3846746	0.92[JPT][hapmap]
rs3846748	1.00[JPT][hapmap]
rs3846750	1.00[JPT][hapmap]
rs3889007	1.00[JPT][hapmap]
rs4283855	1.00[JPT][hapmap]
rs4496758	1.00[JPT][hapmap]
rs6455367	1.00[JPT][hapmap]
rs6455370	1.00[JPT][hapmap]
rs6455371	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs6900840	1.00[JPT][hapmap]
rs6902797	1.00[JPT][hapmap]
rs6902986	1.00[JPT][hapmap]
rs6906572	1.00[JPT][hapmap]
rs6906592	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6910903	1.00[JPT][hapmap]
rs6911812	1.00[JPT][hapmap]
rs6911983	1.00[JPT][hapmap]
rs6913548	1.00[JPT][hapmap]
rs6915405	1.00[JPT][hapmap]
rs6916974	1.00[JPT][hapmap]
rs6917368	1.00[JPT][hapmap]
rs6918393	0.92[JPT][hapmap]
rs6922680	1.00[JPT][hapmap]
rs6926591	1.00[JPT][hapmap]
rs6930397	1.00[JPT][hapmap]
rs6931901	1.00[JPT][hapmap]
rs6933150	1.00[JPT][hapmap]
rs6933784	1.00[JPT][hapmap]
rs6939478	1.00[JPT][hapmap]
rs6939814	1.00[JPT][hapmap]
rs6940416	1.00[JPT][hapmap]
rs6941205	0.92[JPT][hapmap]
rs6942012	1.00[JPT][hapmap]
rs7739098	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7740873	1.00[JPT][hapmap]
rs7741265	1.00[JPT][hapmap]
rs7742044	0.83[AFR][1000 genomes]
rs7743819	1.00[JPT][hapmap]
rs7752409	1.00[JPT][hapmap]
rs7753355	1.00[JPT][hapmap]
rs7757026	1.00[JPT][hapmap]
rs7759464	1.00[JPT][hapmap]
rs7765110	1.00[JPT][hapmap]
rs7766075	1.00[JPT][hapmap]
rs7767109	1.00[JPT][hapmap]
rs7769582	1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[YRI][hapmap]
rs7775962	1.00[JPT][hapmap]
rs9283835	1.00[JPT][hapmap]
rs9294868	1.00[JPT][hapmap]
rs9294872	1.00[JPT][hapmap]
rs9294874	1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs9294876	1.00[JPT][hapmap]
rs9446245	1.00[JPT][hapmap]
rs9446248	1.00[JPT][hapmap]
rs9446267	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs9455092	1.00[JPT][hapmap]
rs9455104	1.00[JPT][hapmap]
rs9455105	1.00[JPT][hapmap]
rs9455113	1.00[JPT][hapmap]
rs9455121	1.00[JPT][hapmap]
rs9455130	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9455132	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9455133	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9455158	0.92[JPT][hapmap]
rs9455160	1.00[JPT][hapmap]
rs9455162	1.00[JPT][hapmap]
rs9455163	1.00[JPT][hapmap]
rs9455167	0.91[JPT][hapmap]
rs9455168	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1026229	chr6:71016272-71183503	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv886144	chr6:71018467-71214201	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1032876	chr6:71048428-71145166	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1027161	chr6:71106657-71145166	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1075262	C6orf57	cis	cerebellum	SCAN
rs1075262	C6orf57	cis	multi-tissue	Pritchard
rs1075262	C6orf57	cis	parietal	SCAN
rs1075262	C6orf57	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71103600-71122400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:71109800-71121400	Weak transcription	K562	blood
3	chr6:71110600-71120400	Weak transcription	Stomach Mucosa	stomach
4	chr6:71116600-71119800	Weak transcription	HepG2	liver
5	chr6:71116800-71122000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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