Variant report

Variant	rs12452094
Chromosome Location	chr17:60007248-60007249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60003458..60007739-chr17:60031552..60035376,4	MCF-7	breast:
2	chr17:60005709..60008113-chr17:60023114..60025647,2	MCF-7	breast:
3	chr17:60005081..60007593-chr3:197685672..197687423,2	MCF-7	breast:
4	chr17:60002606..60006531-chr17:60006987..60012322,8	MCF-7	breast:
5	chr17:60007193..60009605-chr17:60184823..60187423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000114473	Chromatin interaction
ENSG00000185621	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11079459	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12450560	1.00[CEU][hapmap]
rs12451910	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12452732	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12600620	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12600909	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604037	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16945692	0.90[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16945753	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16945756	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16945759	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16945801	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271576	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278812	0.82[JPT][hapmap]
rs28654524	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3744434	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3809753	1.00[CEU][hapmap]
rs3826419	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs4410139	0.84[EUR][1000 genomes]
rs4422036	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs4968408	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968451	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4968452	0.84[AMR][1000 genomes]
rs4968454	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968455	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4968456	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4968457	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968459	0.81[ASN][1000 genomes]
rs4968460	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968461	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968462	0.82[CEU][hapmap];0.83[JPT][hapmap];0.84[AFR][1000 genomes]
rs4968463	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4968464	0.80[AFR][1000 genomes]
rs4968467	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs4968468	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs4968470	0.81[EUR][1000 genomes]
rs4968476	0.91[CEU][hapmap]
rs4988344	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56794817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57746689	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58085921	0.87[ASN][1000 genomes]
rs58241345	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58624595	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59080342	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60053512	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61169879	0.81[AMR][1000 genomes]
rs61658218	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6504084	0.90[CEU][hapmap]
rs7218724	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7221089	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73332565	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73332580	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332598	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73334621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73336436	0.81[EUR][1000 genomes]
rs8065778	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8066964	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8074890	1.00[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8080599	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8081917	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9630735	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9630736	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60005400-60018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:60005800-60017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:60005800-60017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:60005800-60017800	Weak transcription	Primary T cells from cord blood	blood
5	chr17:60005800-60017800	Weak transcription	Adipose Nuclei	Adipose
6	chr17:60005800-60022000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:60005800-60022000	Weak transcription	Thymus	Thymus
8	chr17:60005800-60022800	Weak transcription	Brain Angular Gyrus	brain
9	chr17:60006000-60008200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr17:60006000-60017600	Weak transcription	A549	lung
11	chr17:60006000-60017600	Weak transcription	NH-A	brain
12	chr17:60006000-60017800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:60006000-60017800	Weak transcription	HSMM	muscle
14	chr17:60006000-60018000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:60006000-60018000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr17:60006000-60018400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:60006000-60018600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:60006000-60018600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr17:60006000-60019400	Weak transcription	Hela-S3	cervix
20	chr17:60006000-60019600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr17:60006000-60020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:60006000-60020800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:60006000-60021000	Weak transcription	HMEC	breast
24	chr17:60006000-60021200	Weak transcription	Osteobl	bone
25	chr17:60006000-60021400	Weak transcription	HUVEC	blood vessel
26	chr17:60006000-60022000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr17:60006000-60022000	Weak transcription	Fetal Brain Female	brain
28	chr17:60006000-60022000	Weak transcription	HSMMtube	muscle
29	chr17:60006000-60022800	Weak transcription	Brain Anterior Caudate	brain
30	chr17:60006000-60023000	Weak transcription	Brain Hippocampus Middle	brain
31	chr17:60006000-60023600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:60006200-60018200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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