Variant report

Variant	rs410701
Chromosome Location	chr5:112206416-112206417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112202124..112203911-chr5:112204966..112207266,2	K562	blood:
2	chr5:112196333..112202800-chr5:112202907..112207825,7	MCF-7	breast:
3	chr5:112204419..112206839-chr5:112213966..112216300,2	K562	blood:
4	chr5:112200659..112202447-chr5:112205231..112207652,2	K562	blood:

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1093611	0.92[ASN][1000 genomes]
rs149191	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs149193	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs153544	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs153546	0.90[ASN][1000 genomes]
rs153548	0.90[ASN][1000 genomes]
rs153549	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs153550	0.91[ASN][1000 genomes]
rs153551	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153552	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153556	0.86[EUR][1000 genomes]
rs153557	0.84[EUR][1000 genomes]
rs153561	0.83[EUR][1000 genomes]
rs153563	0.83[EUR][1000 genomes]
rs154344	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2545155	0.86[ASN][1000 genomes]
rs2545156	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545170	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546112	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2546115	0.88[ASN][1000 genomes]
rs3317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351767	0.96[ASN][1000 genomes]
rs351768	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351770	0.94[ASN][1000 genomes]
rs368575	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs373059	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs374613	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs382427	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs395858	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41116	0.82[ASN][1000 genomes]
rs419155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448162	0.83[ASN][1000 genomes]
rs448475	0.82[ASN][1000 genomes]
rs448613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs454968	0.84[ASN][1000 genomes]
rs456531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459102	0.92[ASN][1000 genomes]
rs460137	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs468610	0.82[ASN][1000 genomes]
rs468751	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs468854	0.87[ASN][1000 genomes]
rs469827	0.89[ASN][1000 genomes]
rs469886	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495794	0.96[ASN][1000 genomes]
rs505382	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs514763	0.94[ASN][1000 genomes]
rs566419	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67293732	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712663	0.91[ASN][1000 genomes]
rs712670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213	0.96[ASN][1000 genomes]
rs818426	0.96[EUR][1000 genomes]
rs818428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818429	0.92[ASN][1000 genomes]
rs818430	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818782	0.82[EUR][1000 genomes]
rs818797	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs410701	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs410701	REEP5	cis	Esophagus Muscularis	GTEx
rs410701	REEP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:112198600-112206600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:112198600-112206800	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr5:112198600-112206800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:112198600-112206800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr5:112198600-112207000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr5:112198600-112207000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:112198600-112207400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr5:112198600-112208800	Strong transcription	Fetal Thymus	thymus
12	chr5:112198800-112206800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:112198800-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:112198800-112207200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr5:112198800-112208800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:112199000-112206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:112199000-112207000	Strong transcription	Placenta	Placenta
18	chr5:112199000-112207200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:112199000-112208000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:112199200-112207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:112199200-112210200	Weak transcription	Psoas Muscle	Psoas
23	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
24	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:112199400-112206600	Strong transcription	HSMM	muscle
26	chr5:112199400-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:112199400-112206800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:112199400-112206800	Strong transcription	Fetal Intestine Large	intestine
29	chr5:112199400-112206800	Strong transcription	A549	lung
30	chr5:112199400-112207000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr5:112199400-112207000	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:112199400-112207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:112199400-112207400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:112199400-112207600	Strong transcription	HSMMtube	muscle
35	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
36	chr5:112199600-112206600	Strong transcription	Adipose Nuclei	Adipose
37	chr5:112199600-112206800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr5:112199600-112206800	Strong transcription	NHEK	skin
39	chr5:112199600-112207200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:112199600-112207200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:112199800-112206600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:112199800-112206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:112199800-112212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:112200000-112206600	Strong transcription	Fetal Brain Female	brain
46	chr5:112200000-112206600	Strong transcription	Hela-S3	cervix
47	chr5:112200000-112206800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:112200000-112207600	Strong transcription	Liver	Liver
49	chr5:112200000-112209000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:112200200-112207000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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