Variant report

Variant	rs17135070
Chromosome Location	chr5:112202575-112202576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112201095..112203323-chr5:112277431..112279323,2	K562	blood:
2	chr5:112202124..112203911-chr5:112204966..112207266,2	K562	blood:
3	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10058561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515446	0.81[CHD][hapmap]
rs10515449	0.90[JPT][hapmap]
rs10519333	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11555908	1.00[EUR][1000 genomes]
rs11950612	0.81[CHD][hapmap]
rs12189	0.82[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs13360640	1.00[EUR][1000 genomes]
rs17135066	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17135100	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135108	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135117	0.83[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135149	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135155	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135193	0.82[CHB][hapmap]
rs17164132	0.81[CHD][hapmap]
rs1804197	0.80[ASN][1000 genomes]
rs2304793	0.86[CHD][hapmap]
rs2900065	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3733961	0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs3733963	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822652	0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822654	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3892986	1.00[EUR][1000 genomes]
rs57726881	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57749964	1.00[EUR][1000 genomes]
rs58625991	1.00[EUR][1000 genomes]
rs58865195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59349522	1.00[EUR][1000 genomes]
rs6594652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6864403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6864647	0.82[CHB][hapmap]
rs728344	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73227382	1.00[EUR][1000 genomes]
rs73227383	1.00[EUR][1000 genomes]
rs7701868	0.87[ASN][1000 genomes]
rs7706623	0.81[CHD][hapmap]
rs7728109	0.91[CHB][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7728481	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728766	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7729562	0.82[ASN][1000 genomes]
rs7730241	1.00[EUR][1000 genomes]
rs7735121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9687790	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17135070	REEP5	cis	lymphoblastoid	seeQTL

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	chr5:112198000-112205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:112198600-112205600	Weak transcription	Fetal Brain Male	brain
6	chr5:112198600-112206600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:112198600-112206800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr5:112198600-112206800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:112198600-112206800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr5:112198600-112207000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr5:112198600-112207000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:112198600-112207400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr5:112198600-112208800	Strong transcription	Fetal Thymus	thymus
14	chr5:112198800-112206800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:112198800-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:112198800-112207200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr5:112198800-112208800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:112199000-112206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:112199000-112207000	Strong transcription	Placenta	Placenta
20	chr5:112199000-112207200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:112199000-112208000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112199200-112203400	Weak transcription	Stomach Mucosa	stomach
24	chr5:112199200-112206200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:112199200-112206400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:112199200-112207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:112199200-112210200	Weak transcription	Psoas Muscle	Psoas
28	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
29	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:112199400-112202800	Strong transcription	Brain Germinal Matrix	brain
31	chr5:112199400-112202800	Strong transcription	Fetal Stomach	stomach
32	chr5:112199400-112205000	Weak transcription	Aorta	Aorta
33	chr5:112199400-112205000	Weak transcription	Right Ventricle	heart
34	chr5:112199400-112206600	Strong transcription	HSMM	muscle
35	chr5:112199400-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:112199400-112206800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:112199400-112206800	Strong transcription	Fetal Intestine Large	intestine
38	chr5:112199400-112206800	Strong transcription	A549	lung
39	chr5:112199400-112207000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr5:112199400-112207000	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:112199400-112207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:112199400-112207400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:112199400-112207600	Strong transcription	HSMMtube	muscle
44	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
45	chr5:112199600-112204800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:112199600-112204800	Weak transcription	Gastric	stomach
47	chr5:112199600-112204800	Weak transcription	Left Ventricle	heart
48	chr5:112199600-112205200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:112199600-112205200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:112199600-112206200	Weak transcription	Esophagus	oesophagus

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