Variant report

Variant	rs4444073
Chromosome Location	chr11:10331664-10331665
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9596850..9599628-chr11:10329310..10331865,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238387	Chromatin interaction
ENSG00000166483	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10160247	0.90[JPT][hapmap]
rs10160669	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10500719	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10500720	0.90[JPT][hapmap]
rs10500721	0.86[JPT][hapmap]
rs10500722	0.90[JPT][hapmap]
rs10500723	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs10500724	0.90[JPT][hapmap]
rs10734652	0.92[CEU][hapmap]
rs10743132	0.85[ASN][1000 genomes]
rs10770105	0.90[JPT][hapmap]
rs10770106	0.96[CEU][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs10840369	0.92[CEU][hapmap]
rs10840379	0.85[ASN][1000 genomes]
rs10840384	0.84[ASN][1000 genomes]
rs11042633	0.86[YRI][hapmap]
rs11042656	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042657	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042659	0.81[ASN][1000 genomes]
rs11042661	0.81[ASN][1000 genomes]
rs11042663	0.81[ASN][1000 genomes]
rs11042664	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042666	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042686	0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11042689	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11042702	0.90[JPT][hapmap]
rs11042714	0.90[JPT][hapmap]
rs11042717	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11042721	0.80[JPT][hapmap]
rs11042725	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607174	0.90[JPT][hapmap]
rs11607621	0.85[ASN][1000 genomes]
rs11821308	0.90[JPT][hapmap]
rs12274104	0.90[JPT][hapmap]
rs12275224	0.81[ASN][1000 genomes]
rs12278680	0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12278735	0.90[JPT][hapmap]
rs12280005	0.81[ASN][1000 genomes]
rs12281409	0.82[ASN][1000 genomes]
rs12281526	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12282974	0.82[ASN][1000 genomes]
rs12284884	0.81[ASN][1000 genomes]
rs12286545	0.82[ASN][1000 genomes]
rs12286927	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12287386	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12288200	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12288275	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12288486	0.90[JPT][hapmap]
rs12288654	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12418690	0.85[ASN][1000 genomes]
rs12419064	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442733	0.81[ASN][1000 genomes]
rs1442734	0.80[ASN][1000 genomes]
rs1442736	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs16907462	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs16907471	0.90[JPT][hapmap]
rs16907481	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs16907493	0.90[JPT][hapmap]
rs16907504	0.90[JPT][hapmap]
rs16907533	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs16907561	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs16907564	0.81[ASN][1000 genomes]
rs16907568	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs16907575	0.82[ASN][1000 genomes]
rs16907615	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs16907635	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1822294	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1822295	0.81[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1867136	0.81[ASN][1000 genomes]
rs1867137	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1867138	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2028576	0.90[JPT][hapmap]
rs2060658	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2069214	0.81[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2119991	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2278630	0.90[JPT][hapmap]
rs2278632	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2278633	0.89[JPT][hapmap]
rs2278634	0.90[JPT][hapmap]
rs2957671	0.85[ASN][1000 genomes]
rs2957674	0.85[ASN][1000 genomes]
rs2957699	0.85[ASN][1000 genomes]
rs3178898	0.90[JPT][hapmap]
rs35598338	0.85[ASN][1000 genomes]
rs3814700	0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4076050	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4323860	0.86[JPT][hapmap]
rs4399321	0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs4597056	0.95[JPT][hapmap]
rs4641466	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4910115	0.90[JPT][hapmap]
rs57153895	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57595438	0.81[ASN][1000 genomes]
rs58340019	0.82[ASN][1000 genomes]
rs59717668	0.88[ASN][1000 genomes]
rs60319025	0.81[ASN][1000 genomes]
rs61889798	0.85[ASN][1000 genomes]
rs6484147	0.90[JPT][hapmap]
rs6484148	0.90[JPT][hapmap]
rs6484152	0.90[JPT][hapmap]
rs7107290	0.90[JPT][hapmap]
rs7107727	0.87[ASN][1000 genomes]
rs7108358	0.90[JPT][hapmap]
rs7110312	0.92[CEU][hapmap]
rs7110652	0.90[JPT][hapmap]
rs7118500	0.90[JPT][hapmap]
rs7123728	0.86[JPT][hapmap]
rs7124925	0.95[JPT][hapmap];0.93[YRI][hapmap]
rs7129047	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs721008	0.90[JPT][hapmap]
rs726102	0.90[JPT][hapmap]
rs7479039	0.86[JPT][hapmap]
rs7927874	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933018	0.85[ASN][1000 genomes]
rs7935242	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938543	0.90[JPT][hapmap]
rs7947666	0.90[JPT][hapmap]
rs7952229	0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4444073	DKK3	cis	cerebellum	SCAN
rs4444073	SYT9	cis	cerebellum	SCAN
rs4444073	RP11-351I24.1	cis	Whole Blood	GTEx
rs4444073	LYVE1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10329400-10332200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:10329800-10332400	Enhancers	Fetal Heart	heart
3	chr11:10330000-10331800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:10330000-10331800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:10330000-10331800	Enhancers	Liver	Liver
6	chr11:10330000-10331800	Enhancers	Duodenum Mucosa	Duodenum
7	chr11:10330000-10332200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:10330000-10332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:10330000-10334400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:10330200-10331800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr11:10330200-10331800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:10330200-10331800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr11:10330200-10332000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr11:10330200-10332200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:10330200-10332200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr11:10330200-10332200	Enhancers	HUVEC	blood vessel
17	chr11:10330200-10332400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr11:10330200-10332400	Enhancers	Colon Smooth Muscle	Colon
19	chr11:10330200-10332400	Enhancers	Small Intestine	intestine
20	chr11:10330200-10332400	Enhancers	HMEC	breast
21	chr11:10330200-10332400	Enhancers	K562	blood
22	chr11:10330200-10338600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:10330400-10332400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr11:10330400-10332400	Enhancers	Stomach Mucosa	stomach
25	chr11:10330600-10332000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr11:10330600-10332200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:10330600-10332400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:10330800-10332200	Enhancers	Gastric	stomach
29	chr11:10330800-10332400	Enhancers	Right Atrium	heart
30	chr11:10330800-10339400	Weak transcription	Psoas Muscle	Psoas
31	chr11:10330800-10344400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:10331000-10332000	Weak transcription	Esophagus	oesophagus
33	chr11:10331000-10332000	Enhancers	Fetal Intestine Large	intestine
34	chr11:10331000-10332000	Weak transcription	Fetal Thymus	thymus
35	chr11:10331000-10332000	Weak transcription	Right Ventricle	heart
36	chr11:10331000-10332200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr11:10331000-10332200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:10331000-10332200	Enhancers	NHEK	skin
39	chr11:10331000-10332400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr11:10331000-10332400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr11:10331000-10332400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr11:10331000-10332400	Enhancers	Dnd41	blood
43	chr11:10331000-10336200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:10331000-10340000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:10331000-10340000	Weak transcription	Spleen	Spleen
46	chr11:10331200-10331800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:10331200-10332000	Weak transcription	Left Ventricle	heart
48	chr11:10331200-10332200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:10331200-10332200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:10331200-10332200	Enhancers	Fetal Intestine Small	intestine

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