Variant report

Variant	rs10882962
Chromosome Location	chr10:99308923-99308924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr10:99275110..99276850-chr10:99307857..99310053,2	MCF-7	breast:
4	chr10:99256850..99259396-chr10:99308811..99310601,2	MCF-7	breast:
5	chr10:99307089..99309387-chr10:99309451..99312013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10748698	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748699	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]
rs10748700	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882956	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10882957	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882961	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882963	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10882965	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882966	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1107517	0.81[EUR][1000 genomes]
rs1107518	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11189244	0.82[MEX][hapmap]
rs11189245	0.82[MEX][hapmap]
rs11189253	0.82[CHB][hapmap]
rs11189259	0.88[MEX][hapmap]
rs11189266	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11189270	0.85[EUR][1000 genomes]
rs11189274	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs11189275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189278	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189281	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs11189284	0.90[CEU][hapmap]
rs11511362	0.85[EUR][1000 genomes]
rs11528108	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11528109	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11814566	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs12219064	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12221474	0.93[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12243136	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12415338	0.84[EUR][1000 genomes]
rs12766074	0.84[EUR][1000 genomes]
rs12774288	0.80[EUR][1000 genomes]
rs12775868	0.81[EUR][1000 genomes]
rs12783481	0.85[EUR][1000 genomes]
rs1417408	0.95[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1572860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108059	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282373	0.80[CEU][hapmap]
rs3814554	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3818910	0.90[CEU][hapmap]
rs4635019	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4919104	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap]
rs4919108	0.85[EUR][1000 genomes]
rs4919109	0.81[EUR][1000 genomes]
rs7077211	0.95[ASN][1000 genomes]
rs7077976	0.85[EUR][1000 genomes]
rs7089060	0.83[CHB][hapmap]
rs7094973	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs7342022	0.88[EUR][1000 genomes]
rs7475470	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7475851	0.84[EUR][1000 genomes]
rs7893335	0.82[MEX][hapmap]
rs7902642	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7921278	0.88[ASN][1000 genomes]
rs7921505	0.88[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
rs10882962	WNT8B	cis	cerebellum	SCAN
rs10882962	C10orf28	cis	cerebellum	SCAN
rs10882962	HOGA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99300600-99309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr10:99303000-99327600	Weak transcription	Aorta	Aorta
3	chr10:99303200-99309000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr10:99303200-99327600	Weak transcription	Pancreas	Pancrea
5	chr10:99303400-99309600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:99303600-99309000	Weak transcription	Fetal Heart	heart
7	chr10:99303600-99309400	Weak transcription	Fetal Lung	lung
8	chr10:99303800-99309000	Weak transcription	A549	lung
9	chr10:99303800-99309400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:99303800-99309400	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:99303800-99327800	Weak transcription	Ovary	ovary
12	chr10:99304200-99309200	Weak transcription	NHDF-Ad	bronchial
13	chr10:99304200-99313400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:99305600-99309800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:99305800-99309200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:99306000-99309400	Weak transcription	Lung	lung
17	chr10:99306000-99311000	Enhancers	Fetal Muscle Leg	muscle
18	chr10:99306200-99310000	Enhancers	Brain Cingulate Gyrus	brain
19	chr10:99306200-99310600	Enhancers	Fetal Muscle Trunk	muscle
20	chr10:99306400-99310800	Enhancers	Brain Substantia Nigra	brain
21	chr10:99306400-99311000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr10:99306400-99311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:99306400-99311400	Enhancers	Psoas Muscle	Psoas
24	chr10:99306600-99310800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:99306600-99311400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:99306800-99310400	Enhancers	Right Ventricle	heart
27	chr10:99306800-99310600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:99306800-99310600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:99306800-99310800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:99307000-99309200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:99307000-99309600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:99307000-99309800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr10:99307000-99311400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr10:99307200-99309200	Weak transcription	Right Atrium	heart
35	chr10:99307200-99309600	Weak transcription	HSMMtube	muscle
36	chr10:99307200-99310000	Weak transcription	Fetal Kidney	kidney
37	chr10:99307200-99310000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:99307200-99310000	Weak transcription	Spleen	Spleen
39	chr10:99307200-99313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:99307400-99309000	Weak transcription	Adipose Nuclei	Adipose
41	chr10:99307400-99309600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr10:99307400-99310000	Enhancers	NH-A	brain
43	chr10:99307600-99310800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:99307600-99311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr10:99307600-99311400	Enhancers	HMEC	breast
46	chr10:99307800-99309800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:99307800-99310400	Enhancers	Brain Angular Gyrus	brain
48	chr10:99308000-99309400	Enhancers	Brain Hippocampus Middle	brain
49	chr10:99308000-99310800	Enhancers	Left Ventricle	heart
50	chr10:99308000-99313200	Weak transcription	HUVEC	blood vessel

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