Variant report

Variant	rs10770106
Chromosome Location	chr11:10312077-10312078
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10311957..10313803-chr11:10314378..10316867,2	K562	blood:
2	chr11:10308479..10310637-chr11:10311551..10314059,2	K562	blood:
3	chr11:10308390..10310573-chr11:10310763..10312944,2	MCF-7	breast:
4	chr11:10310003..10312176-chr11:10314204..10316656,4	MCF-7	breast:
5	chr11:10309394..10313803-chr11:10314307..10318397,4	K562	blood:

Variant related genes	Relation type
ENSG00000133812	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10160247	0.90[JPT][hapmap]
rs10160669	0.90[JPT][hapmap]
rs10500719	0.90[JPT][hapmap]
rs10500720	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10500721	0.86[JPT][hapmap]
rs10500722	0.90[JPT][hapmap];0.84[LWK][hapmap];0.89[YRI][hapmap]
rs10500723	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10500724	1.00[ASW][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs10734652	0.89[CEU][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs10743132	0.82[ASN][1000 genomes]
rs10770105	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10840363	0.89[CEU][hapmap]
rs10840364	0.89[CEU][hapmap]
rs10840369	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs10840379	0.82[ASN][1000 genomes]
rs10840384	0.82[ASN][1000 genomes]
rs10840386	0.84[ASN][1000 genomes]
rs11042621	0.89[CEU][hapmap]
rs11042622	0.87[CEU][hapmap]
rs11042652	0.81[ASN][1000 genomes]
rs11042653	0.81[ASN][1000 genomes]
rs11042656	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042657	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042659	0.82[ASN][1000 genomes]
rs11042661	0.82[ASN][1000 genomes]
rs11042663	0.82[ASN][1000 genomes]
rs11042664	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042666	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042686	0.90[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs11042689	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs11042702	1.00[ASW][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap]
rs11042714	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11042717	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs11042719	0.81[ASN][1000 genomes]
rs11042721	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11607174	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11607621	0.82[ASN][1000 genomes]
rs11821308	0.90[JPT][hapmap]
rs12274104	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12275224	0.82[ASN][1000 genomes]
rs12278680	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12278735	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12280005	0.82[ASN][1000 genomes]
rs12281409	0.84[ASN][1000 genomes]
rs12281526	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12282974	0.84[ASN][1000 genomes]
rs12284884	0.82[ASN][1000 genomes]
rs12286545	0.84[ASN][1000 genomes]
rs12286927	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12287386	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12288200	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12288275	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12288486	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12288654	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12291196	0.81[ASN][1000 genomes]
rs12291198	0.81[ASN][1000 genomes]
rs12418494	0.90[ASN][1000 genomes]
rs12418690	0.82[ASN][1000 genomes]
rs1442733	0.82[ASN][1000 genomes]
rs1442734	0.82[ASN][1000 genomes]
rs1442736	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1442738	0.82[YRI][hapmap]
rs1562782	0.81[CEU][hapmap]
rs16907462	0.90[JPT][hapmap]
rs16907471	0.90[JPT][hapmap]
rs16907481	0.90[JPT][hapmap]
rs16907493	0.90[JPT][hapmap]
rs16907504	0.90[JPT][hapmap]
rs16907515	0.83[EUR][1000 genomes]
rs16907519	0.83[EUR][1000 genomes]
rs16907533	0.90[JPT][hapmap]
rs16907544	0.81[ASN][1000 genomes]
rs16907552	0.81[ASN][1000 genomes]
rs16907554	0.81[ASN][1000 genomes]
rs16907561	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907564	0.82[ASN][1000 genomes]
rs16907568	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907575	0.84[ASN][1000 genomes]
rs16907615	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16907635	0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822294	0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822295	0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1867136	0.82[ASN][1000 genomes]
rs1867137	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1867138	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2028576	0.90[JPT][hapmap]
rs2060658	0.80[JPT][hapmap];0.85[YRI][hapmap]
rs2069214	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2119991	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2278630	0.90[JPT][hapmap]
rs2278632	0.90[JPT][hapmap]
rs2278633	0.94[JPT][hapmap]
rs2278634	0.90[JPT][hapmap]
rs2957671	0.82[ASN][1000 genomes]
rs2957674	0.82[ASN][1000 genomes]
rs2957699	0.82[ASN][1000 genomes]
rs3178898	0.90[JPT][hapmap]
rs35598338	0.82[ASN][1000 genomes]
rs3814700	0.85[JPT][hapmap]
rs4323860	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs4399321	0.85[JPT][hapmap]
rs4444073	0.96[CEU][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs4459296	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4531462	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4543988	0.83[EUR][1000 genomes]
rs4597056	1.00[ASW][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.89[YRI][hapmap]
rs4622247	0.83[EUR][1000 genomes]
rs4635071	0.89[CEU][hapmap]
rs4641466	0.85[JPT][hapmap]
rs4910107	0.81[YRI][hapmap]
rs4910115	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs57521137	0.81[ASN][1000 genomes]
rs57522724	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57595438	0.82[ASN][1000 genomes]
rs58340019	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59717668	0.82[AMR][1000 genomes]
rs60319025	0.82[ASN][1000 genomes]
rs61889798	0.82[ASN][1000 genomes]
rs6484147	0.93[ASW][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6484148	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6484152	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6484160	0.81[ASN][1000 genomes]
rs6484161	0.96[ASN][1000 genomes]
rs7107290	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7107727	0.82[AMR][1000 genomes]
rs7108358	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7110312	0.89[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs7110652	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7115944	0.81[YRI][hapmap]
rs7118500	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7123728	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs7124925	0.90[JPT][hapmap]
rs7129047	0.90[JPT][hapmap]
rs7129531	0.83[JPT][hapmap]
rs721008	0.90[JPT][hapmap]
rs726102	1.00[ASW][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap]
rs7479039	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs7933018	0.82[ASN][1000 genomes]
rs7938543	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7945930	0.81[ASN][1000 genomes]
rs7947666	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7950461	0.81[ASN][1000 genomes]
rs7952229	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10770106	DKK3	cis	cerebellum	SCAN
rs10770106	SYT9	cis	cerebellum	SCAN
rs10770106	LYVE1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10290000-10313400	Weak transcription	Fetal Brain Male	brain
2	chr11:10291200-10313600	Weak transcription	NHEK	skin
3	chr11:10291200-10314400	Weak transcription	HSMM	muscle
4	chr11:10298200-10313400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:10299400-10314800	Weak transcription	Small Intestine	intestine
6	chr11:10299800-10314400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:10304000-10312400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:10306400-10313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:10306600-10314400	Weak transcription	Brain Germinal Matrix	brain
10	chr11:10306600-10314800	Weak transcription	Aorta	Aorta
11	chr11:10307000-10313800	Weak transcription	Psoas Muscle	Psoas
12	chr11:10307000-10314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:10307200-10313400	Weak transcription	Fetal Kidney	kidney
14	chr11:10307200-10313400	Weak transcription	HUVEC	blood vessel
15	chr11:10307200-10313800	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:10307200-10314400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:10307400-10313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:10307400-10313400	Weak transcription	Brain Hippocampus Middle	brain
19	chr11:10307600-10313200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:10307600-10314400	Weak transcription	Primary B cells from cord blood	blood
21	chr11:10307600-10314400	Weak transcription	Brain Angular Gyrus	brain
22	chr11:10307800-10313600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:10307800-10314400	Weak transcription	Liver	Liver
24	chr11:10308200-10314400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:10308400-10313800	Weak transcription	Fetal Thymus	thymus
26	chr11:10308400-10314400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:10308600-10312200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:10308600-10314400	Weak transcription	NH-A	brain
29	chr11:10308800-10312200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:10308800-10313200	Weak transcription	Fetal Heart	heart
31	chr11:10308800-10313200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr11:10308800-10314600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr11:10308800-10315000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:10309000-10312200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:10309000-10312200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:10309200-10312200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:10309200-10313400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr11:10309200-10314400	Weak transcription	Brain Substantia Nigra	brain
39	chr11:10309200-10314400	Weak transcription	HSMMtube	muscle
40	chr11:10309400-10314600	Weak transcription	Thymus	Thymus
41	chr11:10310000-10314800	Weak transcription	Left Ventricle	heart
42	chr11:10310200-10312800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:10310200-10313400	Weak transcription	Fetal Brain Female	brain
44	chr11:10310200-10314400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr11:10310400-10312200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:10310400-10313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:10310400-10313800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:10310400-10314400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:10310600-10314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:10310600-10314400	Weak transcription	Rectal Smooth Muscle	rectum

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