Variant report

Variant	rs6715866
Chromosome Location	chr2:38987617-38987618
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	POLR2A	chr2:38987587-38987655	MCF-7	breast:	n/a	n/a
2	CREB1	chr2:38987551-38987832	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
2	chr2:38977221..38979202-chr2:38986373..38988095,2	MCF-7	breast:

Variant related genes	Relation type
TTC39DP	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10173118	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10173240	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10197412	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865144	0.81[EUR][1000 genomes]
rs1138975	0.88[ASN][1000 genomes]
rs11694383	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11898812	0.91[CHB][hapmap]
rs12465043	0.80[EUR][1000 genomes]
rs12469681	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12472454	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473036	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12474770	0.88[ASN][1000 genomes]
rs12477252	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12618118	0.91[CHB][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621103	0.82[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.81[ASN][1000 genomes]
rs12623330	0.81[CEU][hapmap]
rs12991609	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12996194	0.82[EUR][1000 genomes]
rs13011522	0.86[EUR][1000 genomes]
rs13014136	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13024811	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[ASN][1000 genomes]
rs13029406	0.86[ASW][hapmap];0.88[CEU][hapmap];0.83[LWK][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs13383541	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13411868	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13417196	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1529625	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1530852	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1530853	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1979142	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1979143	0.82[CHB][hapmap];0.89[CHD][hapmap]
rs1997377	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2037875	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272445	0.85[TSI][hapmap]
rs3097713	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3097714	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs3099961	0.85[ASN][1000 genomes]
rs3099965	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3099968	0.82[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs3099971	0.88[ASN][1000 genomes]
rs3112140	0.81[EUR][1000 genomes]
rs3112159	0.89[JPT][hapmap]
rs3112178	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3112183	0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[ASN][1000 genomes]
rs3112184	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs3112186	0.88[ASN][1000 genomes]
rs3112188	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs3112189	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs3112191	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs3112192	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs3112194	0.83[ASN][1000 genomes]
rs3112196	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs3112198	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3112200	0.92[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3112204	0.85[ASN][1000 genomes]
rs3112205	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112210	0.86[EUR][1000 genomes]
rs3134628	0.94[CHD][hapmap];0.94[GIH][hapmap];0.83[ASN][1000 genomes]
rs3134629	0.83[ASN][1000 genomes]
rs3134630	0.83[ASN][1000 genomes]
rs3134637	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs35387882	0.93[ASN][1000 genomes]
rs3731838	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs4602206	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4630748	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4670891	0.80[AFR][1000 genomes]
rs4670892	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs4670897	0.81[EUR][1000 genomes]
rs56393601	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62144837	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6717670	0.91[CHB][hapmap]
rs6728394	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs6746818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[ASN][1000 genomes]
rs6753251	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6756847	0.85[TSI][hapmap]
rs7419616	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7419838	0.92[CEU][hapmap]
rs7589162	0.81[CEU][hapmap]
rs7603676	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6715866	DHX57	cis	cerebellum	SCAN
rs6715866	MORN2	cis	parietal	SCAN
rs6715866	DHX57	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38986200-38987800	Enhancers	HepG2	liver

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