Variant report

Variant	rs12222542
Chromosome Location	chr11:75507234-75507235
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75507089..75509212-chr11:75526344..75527964,2	K562	blood:
2	chr11:75505538..75510533-chr11:75511527..75514992,5	MCF-7	breast:
3	chr11:75493435..75496040-chr11:75505908..75507945,2	MCF-7	breast:
4	chr11:75506857..75508473-chr11:75566953..75568870,2	MCF-7	breast:
5	chr11:75475566..75477498-chr11:75506229..75507930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062282	Chromatin interaction
ENSG00000255507	Chromatin interaction
ENSG00000254814	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10160802	0.90[CEU][hapmap]
rs1017713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10219339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793124	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10793125	0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10793126	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10793127	0.94[ASN][1000 genomes]
rs10793132	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793133	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793135	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899105	0.81[ASN][1000 genomes]
rs10899109	0.88[ASN][1000 genomes]
rs10899110	0.93[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10899113	0.94[ASN][1000 genomes]
rs10899114	0.91[CEU][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes]
rs10899115	0.80[AMR][1000 genomes]
rs10899116	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs10899118	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10899119	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899120	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899124	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899127	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899128	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899129	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899131	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899132	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899133	0.97[ASN][1000 genomes]
rs10899134	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899135	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899136	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899137	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899138	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899139	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899140	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899141	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899142	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899144	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899145	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236507	0.80[ASN][1000 genomes]
rs11236508	0.81[ASN][1000 genomes]
rs11236509	0.81[ASN][1000 genomes]
rs11236511	0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs11236514	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11236515	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11236516	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11236517	0.93[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11236518	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11236519	0.94[ASN][1000 genomes]
rs11236526	0.81[AMR][1000 genomes]
rs11236527	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11236528	0.94[ASN][1000 genomes]
rs11236530	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236533	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236537	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236538	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236539	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236540	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236542	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236543	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236545	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236546	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236549	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236551	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236552	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236553	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236554	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236555	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236564	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11501918	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11821808	0.88[ASN][1000 genomes]
rs11822903	0.90[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11823869	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12222995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223234	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12224062	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12278224	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12278257	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12280456	0.91[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12280464	0.90[CEU][hapmap];0.87[JPT][hapmap]
rs12285853	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1458836	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17134394	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1806895	0.88[AMR][1000 genomes]
rs2004638	0.91[CEU][hapmap]
rs2008476	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2168947	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3060	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3740849	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740850	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531117	0.81[CHB][hapmap]
rs57188913	0.88[AMR][1000 genomes]
rs58340821	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58411334	0.94[ASN][1000 genomes]
rs59913369	0.88[AMR][1000 genomes]
rs60677263	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60692776	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs643884	0.81[CHB][hapmap]
rs644361	0.81[CHB][hapmap]
rs6592615	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66784596	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67233017	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67268976	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7101806	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7106736	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7107742	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7108178	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110517	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7118039	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118293	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7118569	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7122123	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7126727	0.82[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7128716	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72995678	0.81[ASN][1000 genomes]
rs72997616	0.94[ASN][1000 genomes]
rs72997623	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72997677	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7933235	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7937642	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7944950	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947418	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7947512	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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
rs12222542	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	chr11:75489200-75508200	Weak transcription	GM12878-XiMat	blood
2	chr11:75495000-75511200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:75495400-75512000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:75496200-75514800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:75496800-75514400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:75497600-75509400	Weak transcription	Primary B cells from cord blood	blood
7	chr11:75497800-75508200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:75497800-75514200	Weak transcription	Gastric	stomach
9	chr11:75498000-75507600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:75498800-75511600	Weak transcription	Stomach Mucosa	stomach
11	chr11:75499000-75512000	Weak transcription	Lung	lung
12	chr11:75499200-75507600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:75501800-75513200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:75502400-75511200	Weak transcription	Esophagus	oesophagus
15	chr11:75503400-75509800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr11:75503800-75507600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:75504400-75508400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:75504400-75512000	Weak transcription	Right Atrium	heart
19	chr11:75504800-75510200	Weak transcription	Fetal Thymus	thymus
20	chr11:75505000-75512200	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:75505600-75509600	Weak transcription	Fetal Heart	heart
22	chr11:75506200-75507400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:75506200-75507600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:75506200-75511400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:75506400-75507400	Enhancers	Right Ventricle	heart
26	chr11:75506400-75507400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:75506400-75507600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:75506400-75507600	Genic enhancers	Adipose Nuclei	Adipose
29	chr11:75506400-75507800	Enhancers	Pancreas	Pancrea
30	chr11:75506400-75508200	Genic enhancers	Fetal Intestine Small	intestine
31	chr11:75506400-75509000	Enhancers	HMEC	breast
32	chr11:75506400-75509400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:75506400-75509400	Enhancers	NHEK	skin
34	chr11:75506400-75514600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:75506600-75507400	Enhancers	Fetal Intestine Large	intestine
36	chr11:75506600-75507600	Enhancers	Duodenum Mucosa	Duodenum
37	chr11:75506600-75508800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:75506800-75509800	Strong transcription	Fetal Stomach	stomach
39	chr11:75507000-75507400	Enhancers	HepG2	liver
40	chr11:75507000-75508000	Enhancers	HUVEC	blood vessel
41	chr11:75507000-75508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:75507000-75508400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:75507000-75508800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:75507000-75509000	Weak transcription	Brain Anterior Caudate	brain
45	chr11:75507000-75509600	Strong transcription	Spleen	Spleen
46	chr11:75507200-75507400	Flanking Active TSS	Liver	Liver
47	chr11:75507200-75508400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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