Variant report

Variant	rs9359748
Chromosome Location	chr6:88095500-88095501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88085614..88089024-chr6:88092671..88096388,4	K562	blood:
2	chr6:88093882..88098127-chr6:88101103..88103625,3	MCF-7	breast:
3	chr6:88092817..88096596-chr6:88116939..88119317,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf164-2	chr6:88091867-88096525	NONHSAT113901

Variant related genes	Relation type
ENSG00000213204	Chromatin interaction
ENSG00000272514	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs107689	0.88[EUR][1000 genomes]
rs107690	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1201409	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs12190280	0.80[EUR][1000 genomes]
rs12207825	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214153	0.86[JPT][hapmap]
rs173333	0.85[EUR][1000 genomes]
rs1753153	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs1753154	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs183599	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs1925695	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs2147918	0.90[CHB][hapmap]
rs2147920	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs2147921	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs2207144	0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs242267	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs242270	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs242278	0.84[EUR][1000 genomes]
rs242279	0.85[EUR][1000 genomes]
rs242280	0.85[EUR][1000 genomes]
rs242281	0.85[EUR][1000 genomes]
rs242283	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs242285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs242286	0.88[EUR][1000 genomes]
rs242287	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2474349	0.82[EUR][1000 genomes]
rs2985039	0.85[EUR][1000 genomes]
rs369674	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3734187	0.90[CHB][hapmap]
rs373646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs376633	0.85[EUR][1000 genomes]
rs3812130	0.90[CHB][hapmap]
rs3812132	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs381782	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs3846776	0.90[CHB][hapmap]
rs3857483	0.90[CHB][hapmap]
rs3857484	0.90[CHB][hapmap]
rs3857488	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs390272	0.82[EUR][1000 genomes]
rs3903920	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs3904088	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs4099964	0.90[CHB][hapmap]
rs4110984	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs445434	0.84[EUR][1000 genomes]
rs446851	0.85[EUR][1000 genomes]
rs447077	0.85[EUR][1000 genomes]
rs448580	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs451089	0.83[EUR][1000 genomes]
rs451465	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs451829	0.84[EUR][1000 genomes]
rs4605853	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs4707346	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs4707347	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4707348	0.90[CHB][hapmap]
rs4707351	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap]
rs4707358	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs586771	0.88[EUR][1000 genomes]
rs59322	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs6454593	0.90[CHB][hapmap]
rs6454630	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs6903219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905947	0.86[JPT][hapmap]
rs6913932	0.90[CHB][hapmap]
rs6914299	0.85[JPT][hapmap]
rs6921007	0.90[CHB][hapmap]
rs6921504	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs6926831	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs6927748	0.89[CHB][hapmap]
rs6933046	0.95[CHB][hapmap]
rs6933587	0.86[JPT][hapmap]
rs6934603	0.90[CHB][hapmap]
rs6940544	0.90[CHB][hapmap]
rs7742478	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7742710	0.82[CHB][hapmap]
rs7746545	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7747129	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752485	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs7755883	0.90[CHB][hapmap]
rs7758618	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs7774603	0.90[CHB][hapmap]
rs7776407	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs910563	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs9294379	0.86[JPT][hapmap]
rs9294381	0.86[JPT][hapmap]
rs9344690	0.81[CHB][hapmap]
rs9344691	0.90[CHB][hapmap]
rs9344693	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs9344695	0.90[CHB][hapmap]
rs9353464	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs9353465	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[TSI][hapmap]
rs9353468	0.90[CHB][hapmap]
rs9353483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9359743	0.90[CHB][hapmap]
rs9359749	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9362411	0.95[CHB][hapmap]
rs9362415	0.90[CHB][hapmap]
rs9362427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450650	0.90[CHB][hapmap]
rs9450652	0.90[CHB][hapmap]
rs9450701	0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9359748	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9359748	SLC35A1	cis	parietal	SCAN
rs9359748	ZNF292	cis	Lymphoblastoid	GTEx
rs9359748	Hs.485895	cis	multi-tissue	Pritchard
rs9359748	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs9359748	C6orf164	cis	Thyroid	GTEx
rs9359748	AKIRIN2	cis	cerebellum	SCAN
rs9359748	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9359748	C6orf164	cis	Whole Blood	GTEx
rs9359748	C6orf162	cis	parietal	SCAN
rs9359748	C6orf162	cis	cerebellum	SCAN
rs9359748	SLC35A1	cis	multi-tissue	Pritchard
rs9359748	SLC35A1	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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