Variant report

Variant	rs10759417
Chromosome Location	chr9:99815929-99815930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99814853..99816502-chr9:99820025..99822075,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10114720	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118886	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118923	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123754	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10123757	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739296	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10759391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759399	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10759400	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759406	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759420	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816926	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10816951	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10816953	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816962	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816963	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816964	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817013	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10980241	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10980243	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10980326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10980346	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10980396	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236690	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12376012	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12376575	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12377546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13285842	0.82[ASN][1000 genomes]
rs15394	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16919034	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16924211	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2004336	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34342973	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4367680	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4501700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4510972	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59995818	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62560873	0.85[ASN][1000 genomes]
rs6477844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035822	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7038926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7857836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7875800	0.94[ASW][hapmap];0.93[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9792463	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[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	nsv1053215	chr9:99483926-99824810	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10759417	SLC35D2	cis	cerebellum	SCAN
rs10759417	HEMGN	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99810200-99818400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:99812600-99816400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:99813600-99816400	Enhancers	Fetal Heart	heart
4	chr9:99814200-99816400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:99814400-99816000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:99814400-99817000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:99814400-99817200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:99814400-99817200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:99814400-99817200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr9:99814600-99816800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:99814600-99817400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:99814800-99816400	Enhancers	Brain Germinal Matrix	brain
13	chr9:99814800-99816800	Weak transcription	Fetal Intestine Large	intestine
14	chr9:99814800-99817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:99815000-99817000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:99815000-99817200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:99815000-99817400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr9:99815200-99816200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:99815200-99817000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:99815200-99817200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr9:99815200-99824400	Weak transcription	Fetal Intestine Small	intestine
22	chr9:99815400-99816200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:99815800-99816000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:99815800-99816200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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