Variant report

Variant	rs3132562
Chromosome Location	chr6:31048992-31048993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30706873..30708855-chr6:31047414..31049286,2	MCF-7	breast:
2	chr6:30582850..30585432-chr6:31048124..31050128,2	K562	blood:
3	chr6:30890243..30892584-chr6:31046594..31049304,2	K562	blood:
4	chr6:30880536..30882349-chr6:31046191..31049160,2	MCF-7	breast:
5	chr6:30795553..30798547-chr6:31047282..31049904,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222894	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2394418	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508014	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517448	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517474	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2517524	0.88[ASN][1000 genomes]
rs2517527	0.86[ASN][1000 genomes]
rs2523856	0.81[AMR][1000 genomes]
rs6457327	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6905484	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9263632	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
10	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
11	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3132562	hmm31752	cis	multi-tissue	Pritchard
rs3132562	HLA-B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:31040600-31055000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:31040600-31062400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:31041600-31053200	Weak transcription	NH-A	brain
5	chr6:31043200-31051200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:31044600-31049800	Weak transcription	HSMMtube	muscle
7	chr6:31046600-31053400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:31047600-31049400	Weak transcription	NHEK	skin
9	chr6:31047600-31051400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:31047600-31051400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:31047600-31051400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:31047600-31051400	Weak transcription	Hela-S3	cervix
13	chr6:31047600-31051400	Weak transcription	HSMM	muscle
14	chr6:31047600-31053800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:31047600-31054600	Weak transcription	A549	lung
16	chr6:31047600-31054800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:31047600-31054800	Weak transcription	Left Ventricle	heart
18	chr6:31047600-31054800	Weak transcription	Right Atrium	heart
19	chr6:31047800-31049200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:31047800-31049400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:31047800-31049800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:31047800-31050800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:31047800-31051000	Weak transcription	Adipose Nuclei	Adipose
24	chr6:31047800-31051200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:31047800-31051200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:31047800-31051200	Weak transcription	NHLF	lung
27	chr6:31047800-31051400	Weak transcription	HMEC	breast
28	chr6:31047800-31051600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:31047800-31051800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:31047800-31053800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:31047800-31054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:31047800-31055000	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:31048000-31050800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:31048000-31051200	Weak transcription	Osteobl	bone
35	chr6:31048000-31051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:31048000-31051600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:31048000-31051600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:31048000-31053400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:31048000-31054200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:31048000-31054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:31048000-31054800	Weak transcription	Dnd41	blood
42	chr6:31048200-31049200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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