Variant report

Variant	rs1998591
Chromosome Location	chr10:96407978-96407979
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	CEBPB	chr10:96407816-96408111	H1-hESC	embryonic stem cell:	n/a	chr10:96407961-96407974 chr10:96407963-96407974 chr10:96407961-96407974 chr10:96407961-96407972
2	RAD21	chr10:96407898-96408106	H1-hESC	embryonic stem cell:	n/a	chr10:96407993-96408000
3	CEBPB	chr10:96407836-96408083	A549	lung:	n/a	chr10:96407961-96407974 chr10:96407963-96407974 chr10:96407961-96407974 chr10:96407961-96407972
4	CEBPB	chr10:96407802-96408115	HepG2	liver:	n/a	chr10:96407961-96407974 chr10:96407963-96407974 chr10:96407961-96407974 chr10:96407961-96407972
5	RAD21	chr10:96407801-96408132	H1-hESC	embryonic stem cell:	n/a	chr10:96407993-96408000
6	USF1	chr10:96407758-96408061	H1-hESC	embryonic stem cell:	n/a	chr10:96407881-96407892
7	CEBPB	chr10:96407891-96408016	K562	blood:	n/a	chr10:96407961-96407974 chr10:96407963-96407974 chr10:96407961-96407974 chr10:96407961-96407972
8	RAD21	chr10:96407900-96408091	H1-hESC	embryonic stem cell:	n/a	chr10:96407993-96408000

Variant related genes	Relation type
CTBP2P2	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1010570	0.87[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10736086	1.00[JPT][hapmap]
rs11188019	0.81[LWK][hapmap]
rs12762067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12772169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12772521	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1326837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555474	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1575934	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1926706	0.85[ASN][1000 genomes]
rs1926707	0.81[ASN][1000 genomes]
rs2094296	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104161	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2104543	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2281889	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2901783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34195517	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34367065	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34870400	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4362080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4501922	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6583952	0.81[ASN][1000 genomes]
rs67482845	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68157779	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7067866	0.81[ASN][1000 genomes]
rs7078811	0.82[LWK][hapmap]
rs749744	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7907009	0.81[ASN][1000 genomes]
rs7912099	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7914753	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7915414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs7916649	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7919273	0.81[ASN][1000 genomes]
rs7919698	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv934280	chr10:96401297-96540495	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1040106	chr10:96405296-96514994	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1040976	chr10:96405296-96516804	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv551954	chr10:96405329-96521249	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv522538	chr10:96405329-96547463	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1049225	chr10:96405502-96516804	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1052478	chr10:96406313-96516804	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1037516	chr10:96407511-96516804	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1047944	chr10:96407825-96563288	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1050653	chr10:96407825-96634161	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1998591	HELLS	cis	cerebellum	SCAN
rs1998591	KIF11	cis	cerebellum	SCAN
rs1998591	C10orf28	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96407400-96413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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