Variant report

Variant	rs2409780
Chromosome Location	chr8:11337587-11337588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11337410..11338246-chr8:11410998..11411873,3	MCF-7	breast:
2	chr8:11337552..11338252-chr8:11411303..11411805,2	K562	blood:
3	chr8:11324797..11325381-chr8:11337437..11337957,2	MCF-7	breast:
4	chr8:11337403..11338287-chr8:11411164..11412225,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154319	Chromatin interaction
ENSG00000254774	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13256690	0.83[ASN][1000 genomes]
rs13277113	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1382568	0.92[ASN][1000 genomes]
rs1478887	0.84[ASN][1000 genomes]
rs1478895	0.81[ASN][1000 genomes]
rs1478901	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1531577	0.82[ASN][1000 genomes]
rs1564267	0.84[ASN][1000 genomes]
rs2061831	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250788	0.81[ASN][1000 genomes]
rs2251056	0.80[ASN][1000 genomes]
rs2254546	0.82[ASN][1000 genomes]
rs2254660	0.81[ASN][1000 genomes]
rs2618444	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618473	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2618476	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2618480	0.81[ASN][1000 genomes]
rs2618481	0.92[ASN][1000 genomes]
rs2736332	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2736336	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2736337	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2736338	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2736340	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2736344	0.81[ASN][1000 genomes]
rs2736345	0.83[ASN][1000 genomes]
rs35393613	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4840565	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4840568	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62489069	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7812879	0.81[ASN][1000 genomes]
rs9693589	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9694294	0.81[ASN][1000 genomes]
rs998682	0.81[ASN][1000 genomes]
rs998683	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762725	chr8:11322997-11350721	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2409780	FAM167A	cis	Whole Blood	GTEx
rs2409780	BLK	cis	multi-tissue	Pritchard
rs2409780	C8orf13	cis	multi-tissue	Pritchard
rs2409780	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs2409780	C8orf13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11332800-11337600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr8:11332800-11337800	Weak transcription	NHLF	lung
3	chr8:11332800-11338000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr8:11332800-11338200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr8:11333000-11337800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:11333000-11337800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:11334800-11339400	Weak transcription	Esophagus	oesophagus
8	chr8:11335000-11338400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr8:11336000-11339800	Enhancers	NHEK	skin
10	chr8:11336200-11339400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:11336200-11343200	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:11336400-11340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:11336600-11339800	Enhancers	NHDF-Ad	bronchial
14	chr8:11336800-11338200	Weak transcription	Primary B cells from cord blood	blood
15	chr8:11337000-11337800	Enhancers	Osteobl	bone
16	chr8:11337000-11339200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:11337000-11339600	Enhancers	NH-A	brain
18	chr8:11337000-11339800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr8:11337000-11339800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:11337000-11339800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr8:11337000-11339800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:11337000-11339800	Enhancers	HMEC	breast
23	chr8:11337200-11337600	Flanking Active TSS	A549	lung
24	chr8:11337200-11338000	Enhancers	Lung	lung
25	chr8:11337200-11338600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr8:11337200-11338800	Enhancers	HUVEC	blood vessel
27	chr8:11337200-11339000	Enhancers	HSMMtube	muscle
28	chr8:11337200-11339600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:11337200-11339600	Enhancers	HSMM	muscle
30	chr8:11337200-11339800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:11337400-11337800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:11337400-11338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:11337400-11338000	Enhancers	Placenta	Placenta
34	chr8:11337400-11338000	Weak transcription	Spleen	Spleen
35	chr8:11337400-11338200	Enhancers	Fetal Thymus	thymus
36	chr8:11337400-11338200	Flanking Active TSS	GM12878-XiMat	blood

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