Variant report

Variant	rs9988874
Chromosome Location	chr11:64113402-64113403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64105656..64108114-chr11:64113236..64114890,2	MCF-7	breast:
2	chr11:64109106..64114264-chr11:64115033..64120054,6	MCF-7	breast:
3	chr11:64111304..64115119-chr11:64121660..64123596,3	MCF-7	breast:
4	chr11:64084147..64086680-chr11:64111827..64113896,2	K562	blood:

Variant related genes	Relation type
ENSG00000126432	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000173113	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10792429	0.87[AMR][1000 genomes]
rs11231745	0.85[ASN][1000 genomes]
rs11231748	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34499953	0.84[ASN][1000 genomes]
rs3782101	0.81[AFR][1000 genomes]
rs4930702	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7107446	0.87[AMR][1000 genomes]
rs953778	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9988817	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
6	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
8	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	237 gene(s)	inside rSNPs	diseases
9	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
10	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
11	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
12	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription 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	178 gene(s)	inside rSNPs	diseases
13	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
14	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
15	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
17	nsv818840	chr11:64097233-64125142	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv818841	chr11:64097233-64129722	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
19	nsv555193	chr11:64107143-64120574	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	22 gene(s)	inside rSNPs	diseases
20	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9988874	HSPC152	Cis_1M	lymphoblastoid	RTeQTL
rs9988874	PRDX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64110000-64114600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:64110000-64115800	Weak transcription	HSMM	muscle
3	chr11:64110000-64122400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:64110200-64117800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:64110200-64125000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:64110200-64125200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:64110400-64114600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
8	chr11:64110600-64113600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:64110600-64113800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:64110600-64113800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:64110800-64113600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:64110800-64114400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr11:64110800-64114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:64110800-64116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:64110800-64116200	Weak transcription	Colonic Mucosa	Colon
16	chr11:64110800-64121400	Strong transcription	Primary T cells from cord blood	blood
17	chr11:64110800-64122400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:64110800-64122400	Weak transcription	Lung	lung
19	chr11:64110800-64122800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:64110800-64123400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:64111000-64113600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:64111000-64114400	Weak transcription	HMEC	breast
23	chr11:64111000-64114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:64111000-64115000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:64111000-64115600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:64111000-64115800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:64111000-64115800	Weak transcription	Adipose Nuclei	Adipose
28	chr11:64111000-64116000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:64111000-64116000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:64111000-64121200	Weak transcription	Liver	Liver
31	chr11:64111000-64121800	Weak transcription	Right Ventricle	heart
32	chr11:64111000-64122400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:64111000-64122400	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:64111000-64122400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:64111000-64122400	Weak transcription	Right Atrium	heart
36	chr11:64111000-64122600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:64111000-64124200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:64111000-64125000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:64111200-64114600	Weak transcription	NHEK	skin
40	chr11:64111200-64115800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:64111200-64116000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:64111200-64116000	Weak transcription	Brain Hippocampus Middle	brain
43	chr11:64111200-64116200	Strong transcription	Fetal Thymus	thymus
44	chr11:64111200-64121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:64111200-64121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:64111200-64122400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:64111400-64113600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:64111400-64114600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:64111400-64114600	Weak transcription	A549	lung
50	chr11:64111400-64114800	Weak transcription	Stomach Mucosa	stomach

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