Variant report

Variant	rs6931295
Chromosome Location	chr6:86144875-86144876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12199873	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs1590281	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065114	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181187	0.85[EUR][1000 genomes]
rs2208725	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229523	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2758840	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2842601	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs2842604	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2842608	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[MKK][hapmap]
rs2842609	1.00[YRI][hapmap]
rs2842612	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2842613	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs4235826	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4235827	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4282381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4304137	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs4351223	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs4373337	0.90[CEU][hapmap]
rs4419647	0.81[ASN][1000 genomes]
rs4441928	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs4501401	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4562107	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579322	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs4593336	0.91[CEU][hapmap]
rs4707207	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454467	0.86[EUR][1000 genomes]
rs6454468	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6454469	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6454471	0.95[CHB][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs6922	0.95[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs7452605	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs7739563	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765636	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770359	0.80[ASN][1000 genomes]
rs9294337	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs9344532	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs9353318	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs9362230	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs9444349	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450272	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450282	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	esv2448290	chr6:86143713-86145103	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6931295	SNHG5	cis	Adipose Subcutaneous	GTEx
rs6931295	SNHG5	cis	Thyroid	GTEx
rs6931295	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs6931295	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs6931295	SNHG5	cis	Whole Blood	GTEx
rs6931295	C6orf160	cis	normal skin	skin_eQTL
rs6931295	SNHG5	cis	multi-tissue	Pritchard
rs6931295	C6orf160	cis	lesional skin	skin_eQTL
rs6931295	C6orf160	cis	uninvolved skin	skin_eQTL
rs6931295	SNHG5	cis	Esophagus Mucosa	GTEx
rs6931295	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs6931295	SNHG5	cis	Artery Tibial	GTEx
rs6931295	SNHG5	cis	Muscle Skeletal	GTEx
rs6931295	SNHG5	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86129800-86157400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:86132400-86145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:86139600-86145000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:86139600-86145200	Weak transcription	NHDF-Ad	bronchial
5	chr6:86141400-86145600	Weak transcription	HepG2	liver
6	chr6:86141800-86145000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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