Variant report

Variant	rs6558521
Chromosome Location	chr8:1700818-1700819
allele	C/T
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	POLR2A	chr8:1700715-1701117	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CLN8	TF binding region

Extended variants
information (count: 117 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10087654	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10095548	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10095696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10097891	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10100341	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10102731	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10105317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106153	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109098	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10113471	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10481354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11136421	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11136422	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11136424	0.88[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11778824	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11986414	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs12335115	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12335117	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12674711	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13251071	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13256424	0.88[ASN][1000 genomes]
rs13261755	0.94[ASN][1000 genomes]
rs13282161	0.88[ASN][1000 genomes]
rs13540	0.90[ASN][1000 genomes]
rs2293977	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28376731	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2957085	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2977197	0.83[ASN][1000 genomes]
rs35062922	0.86[ASN][1000 genomes]
rs3812477	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4242538	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4242539	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4370560	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4372027	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4595147	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4639549	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4875806	0.87[ASN][1000 genomes]
rs4875889	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4875957	0.87[ASN][1000 genomes]
rs4875958	0.88[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4876133	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6558518	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6558520	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6558522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6558523	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6558524	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6558525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6558526	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6558527	0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs6558528	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6558530	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6558531	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6558532	0.92[ASN][1000 genomes]
rs6558533	0.83[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6558534	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6558535	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6981804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982516	0.89[ASN][1000 genomes]
rs6984632	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6986102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6991773	0.89[ASN][1000 genomes]
rs6991783	0.89[ASN][1000 genomes]
rs6993706	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7000162	0.86[ASN][1000 genomes]
rs7001282	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005592	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7005699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7008465	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7014327	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7014823	0.89[ASN][1000 genomes]
rs7015858	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs71499040	0.87[ASN][1000 genomes]
rs730377	0.93[ASN][1000 genomes]
rs730379	0.93[ASN][1000 genomes]
rs7341635	0.88[ASN][1000 genomes]
rs7459507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7460230	0.96[ASN][1000 genomes]
rs7460287	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7460365	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7460866	0.90[ASN][1000 genomes]
rs7460972	0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7461159	0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7461259	0.94[ASN][1000 genomes]
rs7461600	0.86[ASN][1000 genomes]
rs7463876	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7463879	0.92[ASN][1000 genomes]
rs7465178	0.86[ASN][1000 genomes]
rs7818406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822816	0.91[ASN][1000 genomes]
rs7827009	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7827285	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7828950	0.94[ASN][1000 genomes]
rs7838456	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7842425	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7844748	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845723	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs7846610	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9022	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1031375	chr8:1320657-1722050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv889711	chr8:1591412-1904157	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv934075	chr8:1626857-1736355	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1034490	chr8:1654716-1782467	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv609527	chr8:1681733-1753497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
13	nsv870096	chr8:1682851-1767342	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
14	nsv465274	chr8:1685064-1728292	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription 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	8 gene(s)	inside rSNPs	diseases
15	nsv609528	chr8:1685064-1728292	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv532892	chr8:1687433-1839578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	esv2755149	chr8:1689290-1755281	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
18	nsv465275	chr8:1697086-1768004	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
19	nsv609529	chr8:1697086-1768004	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6558521	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs6558521	CLN8	cis	cerebellum	SCAN
rs6558521	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs6558521	CTD-2336O2.1	cis	lung	GTEx
rs6558521	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs6558521	CTD-2336O2.1	cis	Esophagus Muscularis	GTEx
rs6558521	CTD-2336O2.1	cis	Thyroid	GTEx
rs6558521	CLN8	cis	parietal	SCAN
rs6558521	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1692600-1707400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:1694400-1702400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr8:1694400-1702400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:1695200-1703400	Weak transcription	HSMMtube	muscle
5	chr8:1695200-1703400	Weak transcription	NH-A	brain
6	chr8:1695400-1702800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:1695400-1703000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:1695400-1703000	Weak transcription	Placenta	Placenta
9	chr8:1697800-1702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:1700200-1708200	Weak transcription	Pancreas	Pancrea
11	chr8:1700400-1701200	Weak transcription	K562	blood
12	chr8:1700600-1701600	Enhancers	HepG2	liver
13	chr8:1700800-1701400	Enhancers	A549	lung

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