Variant report

Variant	rs548234
Chromosome Location	chr6:106568034-106568035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106565935..106568775-chr6:106582626..106585270,2	MCF-7	breast:
2	chr6:106558728..106560776-chr6:106566123..106570070,3	K562	blood:
3	chr6:106560644..106566595-chr6:106567704..106572815,8	K562	blood:
4	chr6:106562714..106568673-chr6:106569146..106572965,6	K562	blood:
5	chr6:106566135..106570137-chr6:106580831..106586138,5	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1883231	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2005969	0.82[ASN][1000 genomes]
rs4134466	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs498679	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526531	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533733	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7768653	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs802791	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	19838193	GWAS catalog

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106553600-106584000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:106559200-106574200	Weak transcription	Small Intestine	intestine
3	chr6:106565800-106572600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:106566600-106568800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:106566600-106570000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:106566800-106568200	Enhancers	Hela-S3	cervix
7	chr6:106566800-106568600	Enhancers	NHDF-Ad	bronchial
8	chr6:106567000-106568200	Enhancers	NHEK	skin
9	chr6:106567000-106568400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:106567000-106568600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:106567000-106568600	Enhancers	HSMMtube	muscle
12	chr6:106567000-106568800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:106567200-106568200	Enhancers	Fetal Intestine Large	intestine
14	chr6:106567200-106568400	Enhancers	Fetal Heart	heart
15	chr6:106567200-106568400	Weak transcription	Placenta	Placenta
16	chr6:106567200-106573800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:106567400-106568200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:106567400-106568600	Enhancers	Fetal Intestine Small	intestine
19	chr6:106567400-106572800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:106567400-106573400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:106567600-106570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:106567800-106568200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:106567800-106570200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:106567800-106570200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:106567800-106570400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:106567800-106571000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:106568000-106568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:106568000-106570600	Enhancers	GM12878-XiMat	blood
29	chr6:106568000-106576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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