Variant report

Variant	rs55665450
Chromosome Location	chr11:34495807-34495808
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	chr11:34378189..34380818-chr11:34495580..34497533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166016	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10488737	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12421999	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16925614	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16925662	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16925668	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16925673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16925678	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076556	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208675	0.85[ASN][1000 genomes]
rs208677	0.85[ASN][1000 genomes]
rs208680	0.86[ASN][1000 genomes]
rs208681	0.86[ASN][1000 genomes]
rs208682	0.86[ASN][1000 genomes]
rs208683	0.86[ASN][1000 genomes]
rs2231819	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300182	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3758735	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758736	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758737	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758738	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4755374	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756146	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756151	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756155	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4756156	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs489554	0.85[ASN][1000 genomes]
rs55633825	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55941777	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56291727	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs564250	0.87[ASN][1000 genomes]
rs7102889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7104121	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7104394	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7106485	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7109462	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7109778	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7115064	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7126085	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7126243	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130331	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130345	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72923163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924903	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72924928	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72927347	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72927368	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72927369	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7395059	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7928866	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7935626	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938373	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55665450	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs55665450	CAT	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34471400-34496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr11:34471600-34496800	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:34474000-34496800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:34483400-34501600	Weak transcription	HMEC	breast
5	chr11:34487800-34496600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:34487800-34496600	Strong transcription	Hela-S3	cervix
7	chr11:34487800-34497000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:34488000-34496400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:34489400-34496400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:34489400-34496600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:34489400-34496800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:34489600-34496400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:34489600-34496800	Strong transcription	Adipose Nuclei	Adipose
14	chr11:34489800-34496000	Strong transcription	Fetal Stomach	stomach
15	chr11:34489800-34496000	Strong transcription	Left Ventricle	heart
16	chr11:34490000-34496400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:34490200-34497000	Strong transcription	Primary T cells from cord blood	blood
18	chr11:34491000-34497200	Weak transcription	HUVEC	blood vessel
19	chr11:34491000-34501800	Weak transcription	Psoas Muscle	Psoas
20	chr11:34491200-34496000	Weak transcription	NHEK	skin
21	chr11:34491200-34496600	Weak transcription	Fetal Heart	heart
22	chr11:34491200-34497000	Weak transcription	A549	lung
23	chr11:34492000-34498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:34492600-34496200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:34492800-34496600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:34493000-34497800	Weak transcription	Small Intestine	intestine
27	chr11:34493000-34498200	Weak transcription	Esophagus	oesophagus
28	chr11:34493200-34496600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:34493200-34497800	Weak transcription	Dnd41	blood
30	chr11:34493200-34497800	Weak transcription	NHLF	lung
31	chr11:34493200-34498000	Weak transcription	Right Ventricle	heart
32	chr11:34493400-34497200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:34493600-34496600	Weak transcription	Colonic Mucosa	Colon
34	chr11:34493800-34496600	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:34494000-34496600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:34494000-34498000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr11:34494000-34498000	Weak transcription	NHDF-Ad	bronchial
38	chr11:34494000-34498400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:34494000-34498400	Weak transcription	Osteobl	bone
40	chr11:34494000-34499400	Weak transcription	HepG2	liver
41	chr11:34494000-34501800	Weak transcription	HSMM	muscle
42	chr11:34494200-34496400	Weak transcription	NH-A	brain
43	chr11:34494200-34497200	Weak transcription	Brain Germinal Matrix	brain
44	chr11:34494200-34497800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:34494200-34499400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:34494400-34496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:34494400-34496000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:34494400-34496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:34494400-34496200	Weak transcription	Aorta	Aorta
50	chr11:34494400-34496800	Weak transcription	Spleen	Spleen

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