Variant report

Variant	rs6938239
Chromosome Location	chr6:34683635-34683636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNRPC-1	chr6:34683390-34683717	NONHSAT112146

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11752260	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756392	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11759235	0.88[EUR][1000 genomes]
rs1555773	0.88[EUR][1000 genomes]
rs16894959	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1883638	0.82[EUR][1000 genomes]
rs2092344	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395607	0.85[EUR][1000 genomes]
rs2492859	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744937	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744939	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744947	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744954	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744964	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744971	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744972	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744977	0.87[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764203	0.91[EUR][1000 genomes]
rs2764204	0.91[EUR][1000 genomes]
rs2764205	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2814943	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs2814948	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814960	0.88[EUR][1000 genomes]
rs2814962	0.88[EUR][1000 genomes]
rs2814973	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814985	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814986	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814993	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567450	0.92[EUR][1000 genomes]
rs3800457	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56693020	0.88[EUR][1000 genomes]
rs56930444	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59142559	0.88[EUR][1000 genomes]
rs60643641	0.84[EUR][1000 genomes]
rs61431557	0.92[EUR][1000 genomes]
rs6457790	0.92[EUR][1000 genomes]
rs6907508	1.00[ASN][1000 genomes]
rs6911549	0.88[EUR][1000 genomes]
rs6936177	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs73419607	0.86[EUR][1000 genomes]
rs73419621	0.84[EUR][1000 genomes]
rs7755822	0.88[EUR][1000 genomes]
rs7762485	0.84[EUR][1000 genomes]
rs9296130	0.84[EUR][1000 genomes]
rs9462007	1.00[CEU][hapmap]
rs9462012	0.89[EUR][1000 genomes]
rs9462014	0.88[EUR][1000 genomes]
rs9462016	0.92[EUR][1000 genomes]
rs9462025	0.88[EUR][1000 genomes]
rs9462029	0.82[EUR][1000 genomes]
rs9469860	0.94[EUR][1000 genomes]
rs9469864	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9469890	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9469895	0.88[EUR][1000 genomes]
rs9469897	0.84[EUR][1000 genomes]
rs9469900	0.82[EUR][1000 genomes]
rs9469907	0.85[EUR][1000 genomes]
rs9469911	0.87[EUR][1000 genomes]
rs9654581	0.86[EUR][1000 genomes]
rs9688715	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS 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	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised 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	33 gene(s)	inside rSNPs	diseases
10	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv5255	chr6:34658569-34703563	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv508401	chr6:34669708-34710302	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34678000-34686800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:34678000-34686800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:34682400-34684400	Enhancers	A549	lung
4	chr6:34682800-34684800	Weak transcription	K562	blood
5	chr6:34683400-34683800	Enhancers	Stomach Mucosa	stomach
6	chr6:34683400-34683800	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr6:34683400-34685200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:34683400-34686200	Enhancers	NHEK	skin
9	chr6:34683400-34686600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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