Variant report

Variant	rs55888859
Chromosome Location	chr2:55856855-55856856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55852070..55854704-chr2:55855790..55860246,6	K562	blood:
2	chr2:55848892..55851384-chr2:55854717..55856988,2	MCF-7	breast:
3	chr2:55847894..55850021-chr2:55856235..55857780,2	MCF-7	breast:
4	chr2:55843883..55847224-chr2:55855243..55860059,7	MCF-7	breast:
5	chr2:55844845..55846473-chr2:55855751..55857427,2	MCF-7	breast:
6	chr2:55852037..55854671-chr2:55856374..55858421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1013138	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12617627	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12618859	0.80[AFR][1000 genomes]
rs12620407	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12986444	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12992408	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12993624	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12997291	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998780	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12998925	0.92[ASN][1000 genomes]
rs12999506	0.82[AMR][1000 genomes]
rs12999680	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13006502	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13009239	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010217	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13014123	0.89[AMR][1000 genomes]
rs13014898	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13015018	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015030	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015744	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13018767	0.90[AMR][1000 genomes]
rs13021958	0.85[AMR][1000 genomes]
rs13025331	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13027095	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13027803	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1318672	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17800203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34013926	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34143512	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34513671	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34679603	0.82[ASN][1000 genomes]
rs35124901	0.84[AFR][1000 genomes]
rs3791654	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56122729	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66545054	0.85[AMR][1000 genomes]
rs6737995	0.83[AFR][1000 genomes]
rs8080	0.86[AMR][1000 genomes];0.84[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	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55888859	SMEK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
7	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55846800-55858200	Weak transcription	HSMM	muscle
10	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
14	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
15	chr2:55846800-55863400	Weak transcription	NHLF	lung
16	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:55847600-55857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:55847600-55862000	Weak transcription	Osteobl	bone
24	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
25	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
26	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
27	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
28	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:55847800-55862000	Weak transcription	NH-A	brain
31	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel
32	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:55848000-55862600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:55848000-55862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
36	chr2:55848800-55862000	Weak transcription	Hela-S3	cervix
37	chr2:55849000-55857000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:55849200-55857000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:55849200-55858800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:55849200-55858800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:55849200-55862800	Weak transcription	Left Ventricle	heart
42	chr2:55849200-55863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55849200-55865200	Weak transcription	Gastric	stomach
44	chr2:55849200-55865600	Weak transcription	Fetal Brain Female	brain
45	chr2:55849200-55867400	Weak transcription	Lung	lung
46	chr2:55849200-55868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:55849200-55868200	Weak transcription	Right Ventricle	heart
48	chr2:55849200-55869400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:55849400-55857400	Weak transcription	Fetal Intestine Small	intestine

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