Variant report

Variant	rs6695327
Chromosome Location	chr1:174061844-174061845
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:174061646-174061951	T-47D	breast:	n/a	n/a
2	FOXA1	chr1:174061636-174061854	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
RPL30P1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10798302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912719	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912722	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912735	0.89[LWK][hapmap]
rs10912737	0.87[LWK][hapmap]
rs10912751	0.81[LWK][hapmap]
rs12066153	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs12076799	0.85[EUR][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12080977	0.89[LWK][hapmap]
rs12082461	0.89[LWK][hapmap]
rs12092774	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12096785	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12354141	0.89[LWK][hapmap]
rs12563301	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs12563395	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568409	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322780	0.87[CHB][hapmap]
rs13376011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846816	0.87[LWK][hapmap]
rs1799876	0.91[CHB][hapmap]
rs1884994	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs1951627	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs2143114	0.82[CHD][hapmap]
rs4592301	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650945	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs4650989	0.82[CHD][hapmap]
rs4650990	0.82[CHD][hapmap]
rs4652169	0.87[CHB][hapmap]
rs4652234	0.82[CHD][hapmap]
rs4652328	0.85[CEU][hapmap]
rs5878	0.87[CHB][hapmap]
rs61547493	0.82[ASN][1000 genomes]
rs61826843	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826844	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827891	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827894	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425273	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656188	0.82[CHD][hapmap]
rs6661868	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6663875	0.87[CHB][hapmap]
rs6665484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6667267	0.82[CHD][hapmap]
rs6670617	0.82[CHD][hapmap]
rs6673632	0.80[ASN][1000 genomes]
rs6676161	0.89[LWK][hapmap]
rs6677660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678286	0.89[LWK][hapmap]
rs6681390	0.82[CHD][hapmap]
rs6681618	0.82[CHD][hapmap]
rs6686083	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6689285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6696076	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6696163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699146	0.87[CHB][hapmap]
rs714624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs724889	0.89[LWK][hapmap]
rs7413166	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs7511780	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533430	0.83[CHB][hapmap]
rs7535987	0.87[LWK][hapmap]
rs7537517	0.82[CHD][hapmap]
rs7538312	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7553788	0.86[CHB][hapmap]
rs7554915	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs941989	0.87[CHB][hapmap]
rs9425431	0.85[CEU][hapmap]
rs9425433	0.85[CEU][hapmap]
rs972361	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6695327	SNORD78	cis	parietal	SCAN
rs6695327	CENPL	cis	cerebellum	SCAN
rs6695327	PRDX6	cis	parietal	SCAN
rs6695327	C1orf156	cis	parietal	SCAN
rs6695327	SLC9A11	cis	parietal	SCAN
rs6695327	RABGAP1L	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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