Variant report

Variant	rs7804955
Chromosome Location	chr7:64312707-64312708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:64311106..64313068-chr7:64322025..64324713,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-2	chr7:64312177-64314178	NONHSAT121039

Variant related genes	Relation type
ENSG00000213640	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 45 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10255860	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs10258594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10259858	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs10263876	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs10271473	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10949950	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs11769995	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772109	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs11773236	0.87[GIH][hapmap]
rs12532791	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12668689	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13236784	0.87[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1568910	0.87[GIH][hapmap]
rs1568911	0.87[GIH][hapmap]
rs1965558	0.84[CEU][hapmap]
rs2863984	0.84[EUR][1000 genomes]
rs35065007	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4717222	0.87[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4718154	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718163	0.81[TSI][hapmap]
rs4718171	0.81[CHD][hapmap];0.85[GIH][hapmap]
rs6460205	0.81[TSI][hapmap]
rs6460206	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs6460212	0.81[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap]
rs6942993	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960979	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6965861	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6975625	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs6980403	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777724	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809122	0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs7810293	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7811163	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs867630	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
7	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1797468	chr7:64296309-64356050	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:45)

SNP	Gene	Cis/trans	Tissue	Source
rs7804955	ERV3	cis	parietal	SCAN
rs7804955	RP11-797H7.5	cis	Artery Tibial	GTEx
rs7804955	RP11-797H7.3	cis	Artery Tibial	GTEx
rs7804955	SEPHS1P1	cis	Nerve Tibial	GTEx
rs7804955	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs7804955	AC104057.1	cis	Adipose Subcutaneous	GTEx
rs7804955	ZNF273	cis	Heart Left Ventricle	GTEx
rs7804955	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs7804955	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs7804955	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs7804955	ZNF273	cis	parietal	SCAN
rs7804955	SEPHS1P1	cis	Artery Tibial	GTEx
rs7804955	RP11-797H7.5	cis	Thyroid	GTEx
rs7804955	SEPHS1P1	cis	Muscle Skeletal	GTEx
rs7804955	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs7804955	RP11-460N20.5	cis	Thyroid	GTEx
rs7804955	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7804955	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs7804955	RP11-797H7.3	cis	Thyroid	GTEx
rs7804955	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs7804955	RP11-797H7.3	cis	Whole Blood	GTEx
rs7804955	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs7804955	RP11-460N20.5	cis	lung	GTEx
rs7804955	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs7804955	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs7804955	LOC168474	cis	cerebellum	SCAN
rs7804955	ZNF273	cis	Nerve Tibial	GTEx
rs7804955	ZNF273	cis	lung	GTEx
rs7804955	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs7804955	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs7804955	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs7804955	SEPHS1P1	cis	Thyroid	GTEx
rs7804955	RP11-797H7.5	cis	Heart Left Ventricle	GTEx
rs7804955	ZNF273	cis	cerebellum	SCAN
rs7804955	RP11-797H7.5	cis	Esophagus Muscularis	GTEx
rs7804955	RP11-460N20.5	cis	Whole Blood	GTEx
rs7804955	RP11-797H7.3	cis	Artery Aorta	GTEx
rs7804955	RP11-797H7.3	cis	lung	GTEx
rs7804955	RP11-460N20.5	cis	Artery Tibial	GTEx
rs7804955	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs7804955	RP11-797H7.5	cis	lung	GTEx
rs7804955	ZNF138	cis	cerebellum	SCAN
rs7804955	ERV3	cis	multi-tissue	Pritchard
rs7804955	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs7804955	RP11-797H7.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64310400-64312800	Weak transcription	Brain Anterior Caudate	brain
2	chr7:64310400-64313800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:64310400-64320600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:64310600-64313200	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:64311600-64314600	Weak transcription	Stomach Smooth Muscle	stomach

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