Variant report

Variant	rs17163642
Chromosome Location	chr7:10843203-10843204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:10842013..10843817-chr7:10978864..10981804,2	K562	blood:
2	chr7:10838575..10840856-chr7:10841977..10843988,2	MCF-7	breast:
3	chr7:10837164..10840989-chr7:10841354..10845729,6	K562	blood:

Variant related genes	Relation type
ENSG00000189043	Chromatin interaction
ENSG00000271185	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10224975	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10228238	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10247758	0.81[ASN][1000 genomes]
rs10249655	0.89[ASN][1000 genomes]
rs10249916	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10259924	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10950320	0.85[JPT][hapmap]
rs11978329	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983424	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438724	0.89[ASN][1000 genomes]
rs1544411	0.91[ASN][1000 genomes]
rs16876692	0.89[ASN][1000 genomes]
rs17163488	0.87[ASN][1000 genomes]
rs17163678	0.86[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1971642	0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs2040796	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2189535	0.84[ASN][1000 genomes]
rs2189536	0.83[ASN][1000 genomes]
rs2190825	0.81[ASN][1000 genomes]
rs4469352	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4469353	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55706508	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58338658	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61127559	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62438366	0.80[ASN][1000 genomes]
rs62454228	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62454229	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62454235	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460750	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67759012	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960801	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6968151	0.86[CHB][hapmap]
rs6972998	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7777546	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8180724	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9690342	0.90[ASN][1000 genomes]
rs9690372	0.90[ASN][1000 genomes]
rs9690896	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887596	chr7:10493399-10852392	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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 target site	29 gene(s)	inside rSNPs	diseases
3	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1018905	chr7:10679889-10980691	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv2752139	chr7:10798492-10954219	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv887600	chr7:10807685-11090546	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	esv2752140	chr7:10817060-11029748	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17163642	SCIN	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:10842400-10844800	Enhancers	K562	blood
2	chr7:10842800-10843600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr7:10843200-10844400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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