Variant report

Variant	rs3060
Chromosome Location	chr11:75511572-75511573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75511055..75516378-chr11:75524946..75527964,8	MCF-7	breast:
2	chr11:75510774..75513236-chr11:75514739..75516644,2	MCF-7	breast:
3	chr11:75434325..75436917-chr11:75510297..75512123,2	MCF-7	breast:
4	chr11:75510740..75513614-chr11:75516273..75518633,2	MCF-7	breast:
5	chr11:75501785..75503630-chr11:75510335..75512065,2	MCF-7	breast:
6	chr11:75505538..75510533-chr11:75511527..75514992,5	MCF-7	breast:
7	chr11:75505740..75508702-chr11:75509155..75512938,4	K562	blood:

Variant related genes	Relation type
ENSG00000062282	Chromatin interaction
ENSG00000255507	Chromatin interaction
ENSG00000198382	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10160802	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs1017713	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10219339	1.00[CEU][hapmap];0.84[MEX][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10793124	0.81[CEU][hapmap]
rs10793125	0.81[CEU][hapmap]
rs10793132	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10793133	0.95[EUR][1000 genomes]
rs10793135	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10899110	0.81[CEU][hapmap]
rs10899112	0.94[ASN][1000 genomes]
rs10899114	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10899115	0.94[ASN][1000 genomes]
rs10899116	0.90[CEU][hapmap]
rs10899118	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899119	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899120	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899121	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10899122	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10899123	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899124	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10899127	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10899128	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10899129	1.00[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs10899131	0.95[EUR][1000 genomes]
rs10899132	0.95[EUR][1000 genomes]
rs10899134	1.00[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs10899135	0.95[EUR][1000 genomes]
rs10899136	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10899137	0.95[EUR][1000 genomes]
rs10899138	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10899139	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10899140	0.92[EUR][1000 genomes]
rs10899141	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10899142	0.93[EUR][1000 genomes]
rs10899144	0.90[EUR][1000 genomes]
rs10899145	1.00[CEU][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11236511	0.85[MEX][hapmap]
rs11236514	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11236515	0.81[CEU][hapmap]
rs11236516	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11236517	0.85[MEX][hapmap]
rs11236518	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11236525	0.94[ASN][1000 genomes]
rs11236526	0.93[ASN][1000 genomes]
rs11236530	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11236531	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11236533	1.00[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11236534	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11236537	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11236538	0.92[EUR][1000 genomes]
rs11236539	0.95[EUR][1000 genomes]
rs11236540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11236542	0.93[EUR][1000 genomes]
rs11236543	0.93[EUR][1000 genomes]
rs11236545	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11236546	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11236549	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11236551	0.92[EUR][1000 genomes]
rs11236552	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs11236553	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs11236554	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11236555	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs11236564	0.88[EUR][1000 genomes]
rs11501918	0.95[EUR][1000 genomes]
rs11822903	0.88[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11823869	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12222542	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12222995	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12223234	0.88[EUR][1000 genomes]
rs12224062	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12278224	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12278257	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs12280456	0.90[CEU][hapmap]
rs12280464	0.90[CEU][hapmap]
rs12285853	0.95[EUR][1000 genomes]
rs1458836	1.00[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs17134394	1.00[CEU][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs1806895	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2004638	0.90[CEU][hapmap]
rs2008476	0.90[CEU][hapmap];0.92[MEX][hapmap]
rs2168947	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3740849	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3740850	1.00[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs531117	0.80[MEX][hapmap]
rs57188913	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58340821	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59913369	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60677263	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60692776	0.87[EUR][1000 genomes]
rs6592615	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes]
rs66784596	0.93[EUR][1000 genomes]
rs67233017	0.92[EUR][1000 genomes]
rs67268976	0.93[EUR][1000 genomes]
rs7101806	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7106736	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7107742	1.00[CEU][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7108178	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7110517	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7118039	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7118293	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7118569	0.93[EUR][1000 genomes]
rs7122123	0.93[EUR][1000 genomes]
rs7126727	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7128716	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs72997623	0.83[EUR][1000 genomes]
rs72997677	0.92[EUR][1000 genomes]
rs7933235	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7937642	0.92[EUR][1000 genomes]
rs7944950	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7947418	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7947512	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897924	chr11:75424546-75678647	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv897925	chr11:75456134-75556323	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3060	RP11-535A19.1	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75495400-75512000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:75496200-75514800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:75496800-75514400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:75497800-75514200	Weak transcription	Gastric	stomach
5	chr11:75498800-75511600	Weak transcription	Stomach Mucosa	stomach
6	chr11:75499000-75512000	Weak transcription	Lung	lung
7	chr11:75501800-75513200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:75504400-75512000	Weak transcription	Right Atrium	heart
9	chr11:75505000-75512200	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:75506400-75514600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:75507400-75512000	Weak transcription	Right Ventricle	heart
12	chr11:75507400-75512000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:75507400-75512200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:75507600-75512000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:75507600-75512200	Strong transcription	Adipose Nuclei	Adipose
16	chr11:75507800-75511600	Weak transcription	Brain Angular Gyrus	brain
17	chr11:75508000-75514400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:75508200-75514400	Strong transcription	Fetal Intestine Small	intestine
19	chr11:75508400-75513000	Strong transcription	Liver	Liver
20	chr11:75508600-75513000	Strong transcription	Fetal Intestine Large	intestine
21	chr11:75508800-75512000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:75509000-75511800	Weak transcription	Placenta	Placenta
23	chr11:75509000-75511800	Weak transcription	HMEC	breast
24	chr11:75509000-75525200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:75509200-75512000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:75509200-75513800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:75509200-75515600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:75509400-75511600	Weak transcription	GM12878-XiMat	blood
29	chr11:75509400-75511800	Weak transcription	Brain Anterior Caudate	brain
30	chr11:75509400-75511800	Weak transcription	NHEK	skin
31	chr11:75509400-75512000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:75509600-75511800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:75509600-75512000	Weak transcription	Spleen	Spleen
34	chr11:75509600-75513200	Strong transcription	HepG2	liver
35	chr11:75509800-75511800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:75509800-75512000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:75509800-75525000	Weak transcription	Fetal Stomach	stomach
38	chr11:75510200-75512000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr11:75510600-75512600	Weak transcription	Primary B cells from cord blood	blood
40	chr11:75510800-75514400	Enhancers	Fetal Thymus	thymus
41	chr11:75511000-75514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr11:75511200-75512600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:75511200-75512800	Enhancers	Esophagus	oesophagus
44	chr11:75511200-75513000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:75511200-75514000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:75511400-75512000	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr11:75511400-75512000	Enhancers	Brain Cingulate Gyrus	brain

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