Variant report

Variant	rs10748699
Chromosome Location	chr10:99306501-99306502
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	chr10:99255761..99258218-chr10:99306296..99308744,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10748698	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10748700	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882956	0.92[ASN][1000 genomes]
rs10882957	0.95[EUR][1000 genomes]
rs10882959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882961	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882963	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10882965	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882966	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107517	0.86[EUR][1000 genomes]
rs1107518	0.95[EUR][1000 genomes]
rs11189253	0.82[CHB][hapmap]
rs11189259	0.94[MEX][hapmap]
rs11189266	0.92[ASN][1000 genomes]
rs11189270	0.87[EUR][1000 genomes]
rs11189274	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs11189275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189278	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189281	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs11189284	0.90[CEU][hapmap]
rs11511362	0.84[EUR][1000 genomes]
rs11528108	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11528109	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11814566	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12219064	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs12221474	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs12243136	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12355384	0.83[EUR][1000 genomes]
rs12415338	0.83[EUR][1000 genomes]
rs12766074	0.83[EUR][1000 genomes]
rs12774288	0.85[EUR][1000 genomes]
rs12775868	0.81[EUR][1000 genomes]
rs12783481	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1417408	0.95[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1572860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282373	0.80[CEU][hapmap]
rs3814554	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs3818910	0.90[CEU][hapmap]
rs4635019	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919104	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs4919108	0.86[EUR][1000 genomes]
rs4919109	0.86[EUR][1000 genomes]
rs7077211	0.92[ASN][1000 genomes]
rs7077976	0.83[EUR][1000 genomes]
rs7089060	0.83[CHB][hapmap]
rs7094973	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs7342022	0.86[EUR][1000 genomes]
rs7475470	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7475851	0.83[EUR][1000 genomes]
rs7902642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7921253	0.81[ASN][1000 genomes]
rs7921278	0.92[ASN][1000 genomes]
rs7921505	0.92[ASN][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv7508	chr10:99285375-99330501	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10748699	C10orf28	cis	cerebellum	SCAN
rs10748699	HOGA1	cis	lymphoblastoid	seeQTL
rs10748699	WNT8B	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99300600-99306600	Weak transcription	Fetal Kidney	kidney
2	chr10:99300600-99309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:99302200-99308600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:99302600-99308800	Weak transcription	Fetal Thymus	thymus
5	chr10:99303000-99327600	Weak transcription	Aorta	Aorta
6	chr10:99303200-99308400	Weak transcription	HepG2	liver
7	chr10:99303200-99308800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99303200-99309000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:99303200-99327600	Weak transcription	Pancreas	Pancrea
10	chr10:99303400-99306800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr10:99303400-99307800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:99303400-99308000	Enhancers	HUVEC	blood vessel
13	chr10:99303400-99308800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:99303400-99309600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr10:99303600-99306800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:99303600-99306800	Weak transcription	Left Ventricle	heart
17	chr10:99303600-99308800	Weak transcription	Placenta	Placenta
18	chr10:99303600-99308800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:99303600-99309000	Weak transcription	Fetal Heart	heart
20	chr10:99303600-99309400	Weak transcription	Fetal Lung	lung
21	chr10:99303800-99306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:99303800-99306600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:99303800-99306800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:99303800-99306800	Weak transcription	Right Ventricle	heart
25	chr10:99303800-99307600	Weak transcription	Osteobl	bone
26	chr10:99303800-99307800	Weak transcription	Brain Angular Gyrus	brain
27	chr10:99303800-99308600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr10:99303800-99308600	Weak transcription	Brain Anterior Caudate	brain
29	chr10:99303800-99308800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:99303800-99309000	Weak transcription	A549	lung
31	chr10:99303800-99309400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:99303800-99309400	Weak transcription	Colon Smooth Muscle	Colon
33	chr10:99303800-99327800	Weak transcription	Ovary	ovary
34	chr10:99304000-99308600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:99304000-99308600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:99304200-99306800	Weak transcription	Right Atrium	heart
37	chr10:99304200-99307000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:99304200-99307000	Weak transcription	NHLF	lung
39	chr10:99304200-99307600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:99304200-99307600	Weak transcription	HMEC	breast
41	chr10:99304200-99308000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr10:99304200-99309200	Weak transcription	NHDF-Ad	bronchial
43	chr10:99304200-99313400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr10:99304400-99306800	Weak transcription	NH-A	brain
45	chr10:99304400-99307000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:99304400-99307600	Weak transcription	NHEK	skin
47	chr10:99304400-99308600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:99304400-99308800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:99304800-99307000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:99305400-99307200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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