Variant report

Variant	rs10882963
Chromosome Location	chr10:99309958-99309959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99258572..99260331-chr10:99308724..99311083,3	MCF-7	breast:
2	chr10:99299652..99304961-chr10:99307189..99311108,10	MCF-7	breast:
3	chr10:99307089..99309387-chr10:99309451..99312013,2	MCF-7	breast:
4	chr10:99275110..99276850-chr10:99307857..99310053,2	MCF-7	breast:
5	chr10:99256850..99259396-chr10:99308811..99310601,2	MCF-7	breast:
6	chr10:99296840..99298523-chr10:99309435..99312063,2	MCF-7	breast:
7	chr10:99303622..99306407-chr10:99309864..99312001,2	K562	blood:
8	chr10:99223102..99223638-chr10:99309877..99310845,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10748698	0.87[EUR][1000 genomes]
rs10748699	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10748700	0.91[EUR][1000 genomes]
rs10882957	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882959	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10882961	0.91[EUR][1000 genomes]
rs10882962	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10882965	0.93[EUR][1000 genomes]
rs10882966	0.90[EUR][1000 genomes]
rs10882967	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107517	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1107518	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189267	0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11189270	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189274	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189275	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs11189278	0.93[EUR][1000 genomes]
rs11189280	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11189284	0.90[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11511362	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11528108	0.92[EUR][1000 genomes]
rs11528109	0.92[EUR][1000 genomes]
rs11814566	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12219064	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs12221474	0.94[CEU][hapmap];0.83[GIH][hapmap]
rs12243136	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12355384	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12357750	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12415338	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12766074	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12767760	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs12774288	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12775868	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12783481	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1417408	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572860	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs17108059	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2282373	0.80[CEU][hapmap]
rs3814554	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818910	0.90[CEU][hapmap]
rs4244325	0.85[ASN][1000 genomes]
rs4244326	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4635019	0.93[EUR][1000 genomes]
rs4917774	0.86[CHB][hapmap]
rs4919105	0.81[CHB][hapmap]
rs4919108	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4919109	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66521603	0.80[ASN][1000 genomes]
rs68084394	0.92[ASN][1000 genomes]
rs7075656	0.80[CHB][hapmap]
rs7077976	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7094973	0.83[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7342022	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7475470	0.93[EUR][1000 genomes]
rs7475851	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7902642	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs7911122	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10882963	HOGA1	cis	lymphoblastoid	seeQTL
rs10882963	WNT8B	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99303000-99327600	Weak transcription	Aorta	Aorta
2	chr10:99303200-99327600	Weak transcription	Pancreas	Pancrea
3	chr10:99303800-99327800	Weak transcription	Ovary	ovary
4	chr10:99304200-99313400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:99306000-99311000	Enhancers	Fetal Muscle Leg	muscle
6	chr10:99306200-99310000	Enhancers	Brain Cingulate Gyrus	brain
7	chr10:99306200-99310600	Enhancers	Fetal Muscle Trunk	muscle
8	chr10:99306400-99310800	Enhancers	Brain Substantia Nigra	brain
9	chr10:99306400-99311000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr10:99306400-99311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:99306400-99311400	Enhancers	Psoas Muscle	Psoas
12	chr10:99306600-99310800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:99306600-99311400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:99306800-99310400	Enhancers	Right Ventricle	heart
15	chr10:99306800-99310600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:99306800-99310600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:99306800-99310800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:99307000-99311400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:99307200-99310000	Weak transcription	Fetal Kidney	kidney
20	chr10:99307200-99310000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr10:99307200-99310000	Weak transcription	Spleen	Spleen
22	chr10:99307200-99313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr10:99307400-99310000	Enhancers	NH-A	brain
24	chr10:99307600-99310800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:99307600-99311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr10:99307600-99311400	Enhancers	HMEC	breast
27	chr10:99307800-99310400	Enhancers	Brain Angular Gyrus	brain
28	chr10:99308000-99310800	Enhancers	Left Ventricle	heart
29	chr10:99308000-99313200	Weak transcription	HUVEC	blood vessel
30	chr10:99308200-99310400	Weak transcription	Osteobl	bone
31	chr10:99308200-99313200	Weak transcription	NHLF	lung
32	chr10:99308600-99310800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:99308600-99310800	Enhancers	Brain Anterior Caudate	brain
34	chr10:99308600-99311000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:99308600-99311400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:99308600-99311400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:99308600-99311600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr10:99308600-99311800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr10:99308800-99310000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr10:99308800-99310000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:99308800-99310000	Enhancers	Fetal Thymus	thymus
42	chr10:99308800-99310600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:99308800-99310600	Enhancers	HepG2	liver
44	chr10:99308800-99310800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:99308800-99311000	Enhancers	Placenta	Placenta
46	chr10:99308800-99311400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:99308800-99311400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:99309000-99310000	Enhancers	Adipose Nuclei	Adipose
49	chr10:99309000-99310000	Enhancers	Fetal Stomach	stomach
50	chr10:99309000-99310400	Enhancers	Fetal Heart	heart

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