Variant report

Variant	rs6977800
Chromosome Location	chr7:7572215-7572216
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	chr7:7565685..7567431-chr7:7571979..7573747,2	MCF-7	breast:
2	chr7:7571296..7573446-chr7:7605747..7607706,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPA3-3	chr7:7572070-7572765	l_3360_chr7:7558465-7570482_kidney

Variant related genes	Relation type
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10227453	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10236767	0.92[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10486174	0.92[CEU][hapmap]
rs10486178	0.94[CHB][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10486179	0.92[CEU][hapmap];0.81[JPT][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10486182	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10952061	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11767285	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11975180	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs12532693	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12533006	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12702618	0.81[AMR][1000 genomes]
rs13239942	0.82[AMR][1000 genomes]
rs13244586	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13312659	0.92[CEU][hapmap]
rs1544465	0.92[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1544466	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17151557	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[ASN][1000 genomes]
rs17168408	0.94[CHB][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17168446	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17168463	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17168516	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs1971649	0.88[EUR][1000 genomes]
rs2023999	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2108066	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2108069	0.84[EUR][1000 genomes]
rs2214842	0.92[ASN][1000 genomes]
rs2286209	0.84[CEU][hapmap]
rs2348337	0.84[EUR][1000 genomes]
rs2348338	0.86[EUR][1000 genomes]
rs28483212	0.92[ASN][1000 genomes]
rs28553401	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3807856	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3815229	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs3823842	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4720740	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4724999	0.81[CEU][hapmap];0.81[JPT][hapmap];0.91[MKK][hapmap]
rs4725000	0.87[CEU][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap]
rs56412915	0.85[ASN][1000 genomes]
rs60498098	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6943655	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6968507	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6977450	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6977577	0.87[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs720288	0.92[ASN][1000 genomes]
rs73674573	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73674574	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73674578	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73674581	0.88[ASN][1000 genomes]
rs73674582	0.83[ASN][1000 genomes]
rs7459399	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7778306	0.92[CEU][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs7779415	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7784747	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7796700	0.84[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs7803888	0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
16	nsv527573	chr7:7570959-7572215	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6977800	COL28A1	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7528600-7575400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7564200-7575200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:7569400-7575400	Weak transcription	Fetal Kidney	kidney
4	chr7:7570200-7579800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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