Variant report

Variant	rs4630748
Chromosome Location	chr2:38990460-38990461
allele	C/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	CREB1	chr2:38990313-38990759	GM12878	blood:	n/a	n/a
2	CREB1	chr2:38990377-38990715	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
2	chr2:38973025..38976072-chr2:38989424..38992491,3	MCF-7	breast:
3	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
4	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

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

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10173118	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10173240	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs10176932	0.92[ASW][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[MKK][hapmap]
rs10197412	0.96[CEU][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865143	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10865144	0.80[EUR][1000 genomes]
rs11124646	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1138974	0.87[ASN][1000 genomes]
rs11694383	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12469681	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12472454	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12473036	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12477252	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12623330	0.80[CEU][hapmap]
rs12991609	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12996194	0.81[EUR][1000 genomes]
rs13011311	0.84[ASN][1000 genomes]
rs13011522	0.85[EUR][1000 genomes]
rs13014136	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13029406	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs13383541	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs13411868	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13417196	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1529625	0.88[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1530852	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1530853	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1979142	0.88[CEU][hapmap];0.89[CHB][hapmap]
rs1997377	0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2037875	0.96[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2272445	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs2373473	0.90[JPT][hapmap]
rs3099940	0.90[JPT][hapmap]
rs3099941	0.90[JPT][hapmap]
rs3099943	0.81[JPT][hapmap]
rs3099945	0.81[JPT][hapmap]
rs3099952	0.83[ASN][1000 genomes]
rs3099965	0.86[EUR][1000 genomes]
rs3112140	0.80[EUR][1000 genomes]
rs3112198	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3112200	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112205	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112210	0.85[EUR][1000 genomes]
rs3112215	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs3731838	0.81[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs3770681	0.88[CHB][hapmap];0.80[GIH][hapmap]
rs4602206	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670891	0.90[ASN][1000 genomes]
rs56393601	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62144837	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6544175	0.80[ASN][1000 genomes]
rs6715866	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]
rs6728394	0.89[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs6731386	0.84[ASN][1000 genomes]
rs6736004	0.82[ASN][1000 genomes]
rs6746818	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs6753251	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6756847	0.89[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs7419616	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7419838	0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs7581263	0.84[ASN][1000 genomes]
rs7581653	0.84[ASN][1000 genomes]
rs7589162	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs7596239	0.87[ASN][1000 genomes]
rs7603676	0.89[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs7603821	0.84[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4630748	DHX57	cis	cerebellum	SCAN
rs4630748	DHX57	cis	parietal	SCAN
rs4630748	DHX57	cis	multi-tissue	Pritchard
rs4630748	MORN2	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	chr2:38990400-38991200	Enhancers	HepG2	liver

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