Variant report

Variant	rs10115278
Chromosome Location	chr9:96950910-96950911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96945873..96948322-chr9:96948466..96951194,2	MCF-7	breast:
2	chr9:96943921..96946821-chr9:96947982..96950934,2	MCF-7	breast:
3	chr9:96761819..96764816-chr9:96950228..96952225,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10116369	0.81[MKK][hapmap]
rs10117272	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117305	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122644	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821307	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993093	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342389	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345620	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377837	1.00[CHB][hapmap]
rs12378444	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080658	1.00[CHB][hapmap]
rs4744321	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479530	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67631527	0.86[ASN][1000 genomes]
rs7025626	1.00[CHB][hapmap]
rs7038156	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7865658	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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 miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10115278	SLC35D2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:96937200-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:96939800-96960800	Weak transcription	NHDF-Ad	bronchial
4	chr9:96940400-96955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:96941400-96959400	Weak transcription	Spleen	Spleen
6	chr9:96942400-96953200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:96942400-96957600	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:96942400-96964000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:96943000-96952200	Weak transcription	HMEC	breast
10	chr9:96944400-96959400	Weak transcription	Psoas Muscle	Psoas
11	chr9:96945000-96951000	Weak transcription	Brain Angular Gyrus	brain
12	chr9:96945000-96955000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:96945200-96951600	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:96945200-96955200	Weak transcription	Fetal Heart	heart
15	chr9:96946000-96951400	Weak transcription	Brain Substantia Nigra	brain
16	chr9:96946200-96951000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:96946200-96953200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:96946200-96957000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:96946200-96959400	Weak transcription	Aorta	Aorta
20	chr9:96946200-96962800	Weak transcription	Gastric	stomach
21	chr9:96946200-96965000	Weak transcription	NHLF	lung
22	chr9:96946600-96954000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:96946800-96955200	Weak transcription	HSMMtube	muscle
24	chr9:96946800-96955400	Weak transcription	NH-A	brain
25	chr9:96946800-96957200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:96946800-96957800	Weak transcription	Primary T cells from cord blood	blood
27	chr9:96946800-96965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:96947000-96955200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:96947000-96957400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:96947000-96959400	Weak transcription	Left Ventricle	heart
31	chr9:96947000-96959800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:96947000-96966200	Weak transcription	Fetal Kidney	kidney
33	chr9:96947200-96959200	Weak transcription	NHEK	skin
34	chr9:96948000-96951000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:96949400-96951200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:96949400-96952200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:96949400-96960200	Weak transcription	Placenta	Placenta
38	chr9:96949600-96951200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:96949800-96951000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:96949800-96951200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr9:96949800-96957000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:96950000-96955200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:96950000-96955200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:96950000-96955200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:96950000-96955200	Weak transcription	Osteobl	bone
46	chr9:96950600-96951000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr9:96950600-96951200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:96950600-96951200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:96950800-96951000	ZNF genes & repeats	Fetal Lung	lung
50	chr9:96950800-96951200	ZNF genes & repeats	HSMM	muscle

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