Variant report

Variant	rs7744338
Chromosome Location	chr6:88101999-88102000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88093882..88098127-chr6:88101103..88103625,3	MCF-7	breast:
2	chr6:88101491..88103875-chr6:88115341..88119071,3	MCF-7	breast:
3	chr6:87775917..87776730-chr6:88101118..88102031,3	K562	blood:
4	chr6:88096108..88099056-chr6:88101308..88104420,3	K562	blood:
5	chr6:88099705..88102582-chr6:88105005..88107377,3	K562	blood:
6	chr6:88100843..88102348-chr6:88105959..88108612,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203871	Chromatin interaction
ENSG00000272514	Chromatin interaction
ENSG00000213204	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1051550	0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964198	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964212	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964237	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs11966859	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1203155	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1203156	0.94[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1209113	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529410	0.88[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12529423	0.88[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12661245	0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12663865	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13211410	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13211836	0.89[ASN][1000 genomes]
rs13217485	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs173334	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1884320	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs242271	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs242272	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs242273	0.86[EUR][1000 genomes]
rs242291	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs242292	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs242293	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34977536	0.83[ASN][1000 genomes]
rs35332886	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3736740	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs406900	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs414013	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4329082	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4707365	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707367	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707368	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707369	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707370	0.92[ASN][1000 genomes]
rs4707371	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4707372	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5009694	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6454611	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454612	0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6454613	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454614	0.92[ASN][1000 genomes]
rs6454615	0.93[ASN][1000 genomes]
rs6454616	0.88[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6454617	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6454618	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6454621	0.88[ASN][1000 genomes]
rs6454622	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6454623	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6454624	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6454625	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6454626	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6899561	0.90[ASN][1000 genomes]
rs6900397	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs6906433	0.90[ASN][1000 genomes]
rs6907825	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6909168	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6910429	0.88[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6912282	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6912300	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6912442	0.83[ASN][1000 genomes]
rs6912875	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6915562	0.88[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6919775	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6920937	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930072	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930076	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6940716	0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs694524	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7744793	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7746469	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7746876	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7749047	0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7749162	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7753821	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760108	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7761462	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7764266	0.94[ASN][1000 genomes]
rs7764963	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7766462	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767220	0.84[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7773262	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7773804	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs926946	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9294377	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9294378	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9342112	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9344708	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353484	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353486	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353487	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353488	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9362426	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9362428	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9444493	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9444494	0.90[ASN][1000 genomes]
rs9444495	0.92[ASN][1000 genomes]
rs9444496	0.90[ASN][1000 genomes]
rs9450662	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9450672	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs9450674	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450675	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9450676	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450682	0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[ASN][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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7744338	C6orf162	cis	parietal	SCAN
rs7744338	C6orf165	cis	cerebellum	SCAN
rs7744338	C6orf165	cis	parietal	SCAN
rs7744338	C6orf162	cis	cerebellum	SCAN
rs7744338	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88094800-88103400	Weak transcription	K562	blood

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