Variant report

Variant	rs6683945
Chromosome Location	chr1:171840264-171840265
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	chr1:171839647..171841417-chr1:171844666..171847133,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1022541	0.85[ASN][1000 genomes]
rs1040517	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10737338	0.84[ASN][1000 genomes]
rs10753202	0.85[ASN][1000 genomes]
rs10753203	0.83[ASN][1000 genomes]
rs10753204	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10753205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076700	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798695	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798701	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798702	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798705	0.84[ASN][1000 genomes]
rs10798706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798716	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798722	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs10798725	0.85[ASN][1000 genomes]
rs10798726	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs10913908	0.85[ASN][1000 genomes]
rs1118173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808234	0.83[AMR][1000 genomes]
rs12021814	0.83[ASN][1000 genomes]
rs12239702	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405583	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535301	0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs1555100	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs1972340	0.82[ASN][1000 genomes]
rs1980488	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2206543	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235696	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421947	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901600	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500358	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916235	0.84[ASN][1000 genomes]
rs4916400	0.84[ASN][1000 genomes]
rs4916401	0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs4916402	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916403	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916404	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6425454	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425455	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425456	0.84[ASN][1000 genomes]
rs6425468	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6657315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660011	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs6665335	0.84[ASN][1000 genomes]
rs6673646	0.86[CHD][hapmap];0.89[GIH][hapmap]
rs6679341	0.85[ASN][1000 genomes]
rs6685974	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686260	0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs6690848	0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs6701033	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6702944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71523161	0.83[ASN][1000 genomes]
rs742509	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514627	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517331	0.84[ASN][1000 genomes]
rs7526653	0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs7554700	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs7554935	0.85[ASN][1000 genomes]
rs926545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926546	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs965051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS 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 target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6683945	SCYL3	cis	parietal	SCAN
rs6683945	DNM3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171828400-171850800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171837200-171841800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:171838600-171840600	Weak transcription	Brain Substantia Nigra	brain
4	chr1:171838800-171848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:171839000-171844400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:171839400-171840400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:171839800-171842000	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:171840000-171840400	Enhancers	Brain Anterior Caudate	brain
9	chr1:171840000-171840600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:171840000-171841200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:171840200-171840400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:171840200-171840400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:171840200-171840600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:171840200-171842000	Enhancers	HUES48 Cell Line	embryonic stem cell

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