Variant report

Variant	rs11153777
Chromosome Location	chr6:119132164-119132165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119125219..119127915-chr6:119131589..119133462,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10456918	0.88[EUR][1000 genomes]
rs11153778	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11153780	0.88[EUR][1000 genomes]
rs11153791	0.88[EUR][1000 genomes]
rs12190099	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12194135	0.81[EUR][1000 genomes]
rs12194458	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12202077	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12204084	1.00[CEU][hapmap]
rs12204825	0.89[EUR][1000 genomes]
rs12207663	0.88[EUR][1000 genomes]
rs12213327	0.88[EUR][1000 genomes]
rs17506361	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2295709	0.86[CEU][hapmap]
rs284919	0.82[CEU][hapmap]
rs67182660	0.87[EUR][1000 genomes]
rs67456868	0.82[AMR][1000 genomes]
rs6902942	0.88[EUR][1000 genomes]
rs7772912	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs7775275	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs794614	0.86[CEU][hapmap]
rs9374756	0.87[EUR][1000 genomes]
rs9374760	0.88[EUR][1000 genomes]
rs9374762	0.88[EUR][1000 genomes]
rs9401101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[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	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
2	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv886568	chr6:119044453-119132164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv886569	chr6:119055873-119132164	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11153777	BRD7P3	cis	parietal	SCAN
rs11153777	MCM9	cis	cerebellum	SCAN
rs11153777	MCM9	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119108800-119136000	Weak transcription	Aorta	Aorta
2	chr6:119113800-119136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:119116600-119136200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:119121800-119133000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:119121800-119134000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:119121800-119134000	Weak transcription	HSMM	muscle
7	chr6:119121800-119134000	Weak transcription	Osteobl	bone
8	chr6:119121800-119136000	Weak transcription	Fetal Intestine Large	intestine
9	chr6:119122000-119136400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:119122000-119147000	Weak transcription	Stomach Mucosa	stomach
11	chr6:119122200-119133000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:119122200-119135000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:119122200-119136000	Weak transcription	Fetal Intestine Small	intestine
14	chr6:119122200-119136000	Weak transcription	Fetal Stomach	stomach
15	chr6:119122200-119136200	Weak transcription	Esophagus	oesophagus
16	chr6:119122200-119136600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:119122200-119147000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:119122400-119136000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:119122400-119136000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:119122400-119136200	Weak transcription	Pancreas	Pancrea
21	chr6:119122400-119136200	Weak transcription	HepG2	liver
22	chr6:119122400-119136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:119122400-119146800	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:119122600-119136200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:119122600-119144000	Weak transcription	Brain Angular Gyrus	brain
26	chr6:119125600-119136800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:119125600-119143600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:119125800-119134200	Weak transcription	NHEK	skin
29	chr6:119126000-119134200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:119126200-119138800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:119128600-119151600	Weak transcription	Colonic Mucosa	Colon
32	chr6:119128800-119133000	Weak transcription	Fetal Kidney	kidney
33	chr6:119129400-119132400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:119129600-119132200	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:119129600-119132200	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:119129600-119132400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr6:119129800-119132200	Enhancers	Primary T cells from cord blood	blood
38	chr6:119129800-119135000	Weak transcription	Adipose Nuclei	Adipose
39	chr6:119130000-119132200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:119130200-119132200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:119130200-119132200	Enhancers	Fetal Thymus	thymus
42	chr6:119130200-119132200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr6:119130200-119135600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:119130400-119132200	Enhancers	Thymus	Thymus
45	chr6:119130600-119132200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr6:119130600-119132200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr6:119130600-119132800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:119130600-119135800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:119130600-119146400	Weak transcription	Psoas Muscle	Psoas
50	chr6:119130800-119132200	Enhancers	Duodenum Mucosa	Duodenum

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