Variant report

Variant	rs636460
Chromosome Location	chr9:92794721-92794722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92793900..92797470-chr9:92799837..92802623,4	MCF-7	breast:
2	chr9:92794140..92796273-chr9:92804304..92805931,2	MCF-7	breast:
3	chr9:92793117..92794767-chr9:92795692..92798106,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10820832	0.84[AFR][1000 genomes]
rs13296044	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs1373102	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs1443360	0.81[AMR][1000 genomes]
rs35150414	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501675	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs535599	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs557789	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs601472	0.88[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs613212	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs614484	0.81[EUR][1000 genomes]
rs627985	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628020	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs633926	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650415	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650882	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652593	0.80[EUR][1000 genomes]
rs661232	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs666603	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs679273	0.88[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs683669	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7036231	0.83[CHB][hapmap]
rs704476	0.88[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816526	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs920752	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv893562	chr9:92794721-92850878	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs636460	SEMA4D	cis	parietal	SCAN
rs636460	CKS2	cis	cerebellum	SCAN
rs636460	ANKRD19	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92788400-92794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:92789600-92806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:92789800-92796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:92789800-92796400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:92789800-92799600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:92790000-92796400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:92792600-92795600	Enhancers	Brain Germinal Matrix	brain
8	chr9:92793000-92796400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:92793200-92795600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:92793200-92796400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:92793200-92796400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:92793200-92796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:92793600-92796600	Enhancers	Liver	Liver
14	chr9:92793800-92796800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:92794600-92795000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr9:92794600-92795200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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