Variant report

Variant	rs10798706
Chromosome Location	chr1:171820018-171820019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171770266..171771184-chr1:171819765..171820356,3	MCF-7	breast:
2	chr1:171815099..171817651-chr1:171819737..171821446,2	K562	blood:
3	chr1:171709728..171712321-chr1:171818164..171820983,2	K562	blood:
4	chr1:171819236..171820224-chr11:28249477..28250287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1022541	0.82[ASN][1000 genomes]
rs1040517	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs10737338	0.83[ASN][1000 genomes]
rs10753202	0.82[ASN][1000 genomes]
rs10753203	0.80[ASN][1000 genomes]
rs10753204	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs10753205	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1076700	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798695	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798701	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798702	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798705	0.83[ASN][1000 genomes]
rs10798716	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798722	0.84[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs10798725	0.82[ASN][1000 genomes]
rs10798726	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs10913908	0.82[ASN][1000 genomes]
rs1118173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808234	0.88[AMR][1000 genomes]
rs12021814	0.80[ASN][1000 genomes]
rs12239702	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12405583	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535301	0.84[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs1555100	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs1980488	0.84[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs2206543	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];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235696	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2901600	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];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500358	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916235	0.83[ASN][1000 genomes]
rs4916400	0.83[ASN][1000 genomes]
rs4916401	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs4916402	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916403	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916404	0.84[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs6425454	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425456	0.83[ASN][1000 genomes]
rs6425468	0.84[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs6657315	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660011	0.84[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs6665335	0.83[ASN][1000 genomes]
rs6673646	0.86[CHD][hapmap];0.89[GIH][hapmap]
rs6679341	0.82[ASN][1000 genomes]
rs6683945	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]
rs6685974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686260	0.84[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs6690848	0.84[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs6701033	0.81[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71523161	0.80[ASN][1000 genomes]
rs742509	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514627	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7517331	0.83[ASN][1000 genomes]
rs7526653	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs7554700	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs7554935	0.82[ASN][1000 genomes]
rs926545	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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
rs10798706	SCYL3	cis	parietal	SCAN
rs10798706	DNM3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171812200-171833200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:171814600-171833400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:171815800-171820200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:171816400-171820200	Enhancers	Brain Anterior Caudate	brain
5	chr1:171819200-171820400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:171819200-171820400	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:171819400-171820400	Enhancers	Brain Substantia Nigra	brain
8	chr1:171819600-171832800	Weak transcription	Left Ventricle	heart
9	chr1:171819800-171820400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:171819800-171820400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:171819800-171820600	Enhancers	Brain Angular Gyrus	brain
12	chr1:171820000-171820400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:171820000-171820400	Enhancers	Fetal Intestine Small	intestine
14	chr1:171820000-171821000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:171820000-171822200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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