Variant report

Variant	rs2060658
Chromosome Location	chr11:10333849-10333850
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	chr11:10329230..10331779-chr11:10333436..10335756,2	K562	blood:

Variant related genes	Relation type
ENSG00000133805	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10160247	0.91[JPT][hapmap]
rs10160669	0.90[JPT][hapmap]
rs10500719	0.90[JPT][hapmap]
rs10500720	0.90[JPT][hapmap]
rs10500721	0.86[JPT][hapmap]
rs10500722	0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs10500723	0.86[JPT][hapmap]
rs10500724	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10743131	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743133	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10770105	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10770106	0.80[JPT][hapmap];0.85[YRI][hapmap]
rs10840381	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840382	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840385	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042656	0.90[JPT][hapmap]
rs11042657	0.91[JPT][hapmap]
rs11042664	0.91[JPT][hapmap]
rs11042666	0.90[JPT][hapmap]
rs11042686	0.90[JPT][hapmap]
rs11042687	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042689	0.90[JPT][hapmap]
rs11042702	0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042703	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042712	0.83[AMR][1000 genomes]
rs11042714	0.96[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042716	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042717	0.90[JPT][hapmap]
rs11042719	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042721	0.81[JPT][hapmap]
rs11607174	0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11821308	0.90[JPT][hapmap]
rs12274104	0.91[JPT][hapmap]
rs12278680	0.90[JPT][hapmap]
rs12278735	0.91[JPT][hapmap]
rs12279861	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12281526	0.91[JPT][hapmap]
rs12286927	0.90[JPT][hapmap]
rs12287386	0.90[JPT][hapmap]
rs12288200	0.90[JPT][hapmap]
rs12288275	0.90[JPT][hapmap]
rs12288486	0.91[JPT][hapmap]
rs12288654	0.90[JPT][hapmap]
rs12290748	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12419064	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12419593	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442736	0.91[JPT][hapmap]
rs1442738	0.89[CEU][hapmap]
rs16907462	0.91[JPT][hapmap]
rs16907471	0.91[JPT][hapmap]
rs16907481	0.90[JPT][hapmap]
rs16907493	0.90[JPT][hapmap]
rs16907504	0.91[JPT][hapmap]
rs16907533	0.90[JPT][hapmap]
rs16907561	0.90[JPT][hapmap]
rs16907568	0.90[JPT][hapmap]
rs16907615	0.91[JPT][hapmap]
rs16907635	0.90[JPT][hapmap]
rs1822294	0.91[JPT][hapmap]
rs1822295	0.90[JPT][hapmap]
rs1867137	0.90[JPT][hapmap]
rs1867138	0.90[JPT][hapmap]
rs2028576	0.90[JPT][hapmap]
rs2044143	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2044144	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2069214	0.90[JPT][hapmap]
rs2083715	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2119991	0.90[JPT][hapmap]
rs2278630	0.91[JPT][hapmap]
rs2278632	0.90[JPT][hapmap]
rs2278633	0.90[JPT][hapmap]
rs2278634	0.91[JPT][hapmap]
rs3178898	0.91[JPT][hapmap]
rs34051776	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34087225	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34692066	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34739790	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35737881	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36167833	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36170347	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3814700	0.95[JPT][hapmap]
rs4076050	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4323860	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs4399321	0.95[JPT][hapmap]
rs4418806	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4442543	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4444073	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4597056	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4641466	0.95[JPT][hapmap]
rs4910097	0.85[CEU][hapmap]
rs4910107	0.89[CEU][hapmap]
rs4910115	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55933041	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56063978	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56776911	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6484147	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6484148	0.96[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6484152	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6484160	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7107040	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7107290	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7107399	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7107951	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7108358	0.96[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7110652	0.96[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7115944	0.88[CEU][hapmap]
rs7116147	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7118500	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7123728	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7124925	0.95[JPT][hapmap]
rs7129047	0.91[JPT][hapmap]
rs716803	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs721008	0.91[JPT][hapmap]
rs726102	0.92[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7479039	0.96[CEU][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs7924631	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938543	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7944706	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs7945930	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7947666	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7950461	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7952105	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9735682	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2060658	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10330000-10334400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:10330200-10338600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:10330800-10339400	Weak transcription	Psoas Muscle	Psoas
4	chr11:10330800-10344400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:10331000-10336200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:10331000-10340000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:10331000-10340000	Weak transcription	Spleen	Spleen
8	chr11:10331200-10336000	Weak transcription	Osteobl	bone
9	chr11:10331200-10338600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:10331200-10338600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:10331400-10336200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:10331400-10343800	Weak transcription	NHLF	lung
13	chr11:10331800-10338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:10331800-10338600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:10331800-10339000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:10331800-10344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:10332000-10335800	Weak transcription	A549	lung
18	chr11:10332000-10336000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:10332200-10336200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:10332200-10336200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:10332200-10338400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:10332200-10338600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:10332200-10338600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:10332200-10338600	Weak transcription	Left Ventricle	heart
25	chr11:10332400-10336000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:10332400-10336000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:10332400-10338400	Weak transcription	Fetal Thymus	thymus
28	chr11:10332400-10338600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:10332400-10338600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:10332400-10338600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:10332400-10338600	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:10332400-10338600	Weak transcription	Ovary	ovary
33	chr11:10332400-10340000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:10332400-10340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:10332600-10336000	Weak transcription	HepG2	liver
36	chr11:10333000-10334400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:10333800-10334000	Enhancers	Small Intestine	intestine

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