Variant report

Variant	rs3094023
Chromosome Location	chr6:30507920-30507921
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	chr6:30507227..30509019-chr6:30523712..30525596,2	MCF-7	breast:
2	chr6:30455622..30459464-chr6:30506814..30514144,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204592	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes]
rs3094717	0.80[AMR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3132616	0.82[EUR][1000 genomes]
rs3132619	0.80[AMR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262143	0.84[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
7	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
8	nsv884090	chr6:30497652-30510992	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3094023	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30496400-30513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:30497600-30513400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30500400-30509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:30500600-30509200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:30500600-30509400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:30500800-30509200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:30500800-30509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:30501600-30509400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:30501800-30509200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:30505400-30513800	Weak transcription	Gastric	stomach
11	chr6:30507400-30509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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