Variant report

Variant	rs55742873
Chromosome Location	chr2:46873194-46873195
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46870874..46873368-chr2:46874552..46876538,3	K562	blood:
2	chr2:46870874..46873368-chr2:46874552..46876538,2	K562	blood:
3	chr2:46871091..46873562-chr2:46875549..46877733,2	MCF-7	breast:
4	chr2:46872190..46873901-chr2:47005919..47008590,2	K562	blood:
5	chr2:46857941..46860814-chr2:46872610..46874404,2	MCF-7	breast:
6	chr2:46843422..46845727-chr2:46872931..46874613,3	MCF-7	breast:
7	chr2:46861539..46864465-chr2:46873004..46877415,5	MCF-7	breast:
8	chr2:46872495..46874222-chr2:46874302..46877114,2	MCF-7	breast:
9	chr2:46867092..46870472-chr2:46872248..46874879,4	MCF-7	breast:
10	chr2:46842547..46845203-chr2:46873020..46875876,4	MCF-7	breast:
11	chr2:46872845..46875146-chr2:46877009..46879600,2	K562	blood:
12	chr2:46864993..46867053-chr2:46871830..46874793,2	K562	blood:
13	chr2:46872423..46876181-chr2:46924368..46927720,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10495934	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13024534	0.86[ASN][1000 genomes]
rs13406427	0.97[ASN][1000 genomes]
rs13417558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1378764	0.82[ASN][1000 genomes]
rs17767994	0.86[ASN][1000 genomes]
rs17768018	0.86[ASN][1000 genomes]
rs17768132	0.86[ASN][1000 genomes]
rs17768138	0.86[ASN][1000 genomes]
rs17768226	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819022	0.82[ASN][1000 genomes]
rs1824050	0.82[ASN][1000 genomes]
rs2122715	0.82[ASN][1000 genomes]
rs34449783	0.86[ASN][1000 genomes]
rs34748737	0.86[ASN][1000 genomes]
rs34752561	0.82[ASN][1000 genomes]
rs34996358	0.84[ASN][1000 genomes]
rs35449212	0.84[ASN][1000 genomes]
rs35682608	0.82[ASN][1000 genomes]
rs35837037	0.86[ASN][1000 genomes]
rs35949012	0.86[ASN][1000 genomes]
rs4952837	0.86[ASN][1000 genomes]
rs62136873	0.86[ASN][1000 genomes]
rs62136894	0.86[ASN][1000 genomes]
rs62136895	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62136898	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6746598	0.86[ASN][1000 genomes]
rs7565274	0.82[ASN][1000 genomes]
rs7605089	0.97[ASN][1000 genomes]
rs896212	0.86[ASN][1000 genomes]
rs982395	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55742873	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs55742873	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:46854800-46878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:46858000-46874800	Weak transcription	Liver	Liver
4	chr2:46862400-46877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:46869400-46883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:46869600-46876800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:46869600-46881200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:46869800-46878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:46869800-46882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:46870000-46877200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:46870000-46880800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:46870200-46889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:46870400-46878200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:46870800-46873400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:46870800-46873400	Enhancers	Hela-S3	cervix
17	chr2:46870800-46873600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:46870800-46874600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:46870800-46874600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:46870800-46876000	Enhancers	Osteobl	bone
21	chr2:46870800-46876400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:46871000-46874400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:46871000-46874400	Enhancers	NHDF-Ad	bronchial
24	chr2:46871000-46877400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:46871200-46874000	Enhancers	HSMMtube	muscle
26	chr2:46871400-46876000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:46871600-46875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:46871600-46876200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:46871800-46873400	Enhancers	Adipose Nuclei	Adipose
30	chr2:46871800-46873400	Enhancers	Fetal Stomach	stomach
31	chr2:46871800-46873400	Enhancers	Rectal Smooth Muscle	rectum
32	chr2:46871800-46873400	Flanking Active TSS	A549	lung
33	chr2:46871800-46873600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:46871800-46873600	Enhancers	Fetal Lung	lung
35	chr2:46871800-46873800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:46871800-46874200	Enhancers	NH-A	brain
37	chr2:46871800-46874400	Enhancers	NHLF	lung
38	chr2:46871800-46875400	Enhancers	HMEC	breast
39	chr2:46871800-46876000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:46872000-46873200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:46872000-46875800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:46872000-46883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:46872200-46873400	Enhancers	HepG2	liver
44	chr2:46872200-46873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:46872400-46873800	Enhancers	Fetal Muscle Leg	muscle
46	chr2:46872600-46873200	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:46872600-46873400	Enhancers	Brain Anterior Caudate	brain
48	chr2:46872600-46873400	Enhancers	Colon Smooth Muscle	Colon
49	chr2:46872600-46873800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:46872600-46873800	Enhancers	Skeletal Muscle Male	skeletal muscle

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