Variant report

Variant	rs3132611
Chromosome Location	chr6:30541852-30541853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr6:30541629-30541893	GM12878	blood:	n/a	chr6:30541814-30541825

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30455964..30458149-chr6:30539664..30541903,3	MCF-7	breast:
2	chr6:30541727..30544215-chr6:30582444..30584510,3	MCF-7	breast:

Variant related genes	Relation type
ABCF1	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs3094092	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129996	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3130000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130245	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3131110	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3132587	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9262081	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3132611	HLA-DRB5	cis	multi-tissue	Pritchard
rs3132611	VARSL	cis	multi-tissue	Pritchard
rs3132611	HLA-C	cis	multi-tissue	Pritchard
rs3132611	MDC1	cis	multi-tissue	Pritchard
rs3132611	FLJ35429	cis	multi-tissue	Pritchard
rs3132611	HCG22	cis	lymphoblastoid	seeQTL
rs3132611	HLA-F	cis	multi-tissue	Pritchard
rs3132611	HCG27	cis	multi-tissue	Pritchard
rs3132611	HLA-H	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30540000-30542000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:30540000-30544400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30540000-30544400	Weak transcription	Ovary	ovary
4	chr6:30540000-30545400	Weak transcription	Aorta	Aorta
5	chr6:30540200-30542200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:30540200-30542200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:30540200-30542200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:30540200-30542200	Enhancers	Right Atrium	heart
9	chr6:30540200-30542400	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr6:30540200-30542600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:30540200-30542600	Enhancers	Liver	Liver
12	chr6:30540200-30542800	Enhancers	Stomach Mucosa	stomach
13	chr6:30540200-30543200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:30540200-30543600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:30540200-30543600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:30540200-30544600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:30540200-30544600	Weak transcription	Fetal Kidney	kidney
18	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:30540400-30542000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:30540400-30542000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr6:30540400-30542000	Enhancers	NH-A	brain
23	chr6:30540400-30542000	Enhancers	NHDF-Ad	bronchial
24	chr6:30540400-30542400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:30540400-30542400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:30540400-30542400	Enhancers	Adipose Nuclei	Adipose
27	chr6:30540400-30542400	Enhancers	Brain Germinal Matrix	brain
28	chr6:30540400-30542600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:30540400-30542600	Enhancers	Colon Smooth Muscle	Colon
30	chr6:30540400-30542800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:30540400-30543200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:30540400-30543200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:30540400-30543400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:30540400-30543600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr6:30540400-30543800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:30540400-30544400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:30540400-30544400	Weak transcription	HSMMtube	muscle
38	chr6:30540400-30563000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:30540600-30542200	Genic enhancers	NHEK	skin
40	chr6:30540600-30543600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:30540800-30542000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:30540800-30542200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:30540800-30542400	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:30540800-30542400	Genic enhancers	Thymus	Thymus
45	chr6:30540800-30542600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:30540800-30542600	Genic enhancers	Fetal Thymus	thymus
47	chr6:30540800-30543200	Weak transcription	Fetal Lung	lung
48	chr6:30540800-30543800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:30540800-30560800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr6:30540800-30563600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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