Variant report

Variant	rs1738264
Chromosome Location	chr6:38742708-38742709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38742135..38744348-chr6:38746866..38748899,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12173602	0.83[ASN][1000 genomes]
rs1612377	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1615744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678639	0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1678642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678643	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678652	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678654	0.91[ASN][1000 genomes]
rs1678655	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678656	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1678658	0.86[ASN][1000 genomes]
rs1678659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678662	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678672	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678673	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678677	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678678	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678679	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs1678684	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1678736	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738174	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1738175	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1738176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738179	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738180	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738181	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738182	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738251	0.96[ASN][1000 genomes]
rs1738252	0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738253	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738254	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738255	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738256	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738261	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738262	0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738265	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738267	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1738268	0.89[ASN][1000 genomes]
rs1738269	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2448400	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448401	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714178	0.86[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[ASN][1000 genomes]
rs58817640	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9357280	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394532	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1738264	DNAH8	cis	lymphoblastoid	seeQTL
rs1738264	TSPO2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38739400-38746600	Weak transcription	K562	blood
2	chr6:38739600-38744600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:38739800-38743800	Weak transcription	NHEK	skin
4	chr6:38739800-38744200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38739800-38744200	Weak transcription	HUVEC	blood vessel
6	chr6:38739800-38744400	Weak transcription	HMEC	breast
7	chr6:38740200-38743800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:38741000-38744600	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:38741800-38743800	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:38742400-38743400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:38742600-38742800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:38742600-38743000	Enhancers	Primary B cells from cord blood	blood
13	chr6:38742600-38743200	Enhancers	Monocytes-CD14+_RO01746	blood

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