Variant report

Variant	rs17135100
Chromosome Location	chr5:112214655-112214656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112213045..112215334-chr5:112215360..112217961,2	K562	blood:
2	chr5:112213405..112216248-chr5:112216805..112218995,2	K562	blood:
3	chr5:112214521..112217440-chr5:112219552..112222525,2	MCF-7	breast:
4	chr5:112214124..112215918-chr5:112256466..112258811,2	MCF-7	breast:
5	chr5:112204419..112206839-chr5:112213966..112216300,2	K562	blood:
6	chr5:112210185..112212366-chr5:112214528..112217503,2	K562	blood:
7	chr5:112195269..112200241-chr5:112214225..112218967,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249947	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10058561	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10515446	0.81[CHD][hapmap]
rs10515449	0.90[JPT][hapmap]
rs10519333	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11555908	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11950612	0.81[CHD][hapmap]
rs12189	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs13360640	1.00[EUR][1000 genomes]
rs17135066	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17135070	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	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[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]
rs17135117	0.83[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135149	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135155	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135193	0.82[CHB][hapmap]
rs17164132	0.81[CHD][hapmap]
rs2304793	0.86[CHD][hapmap]
rs2900065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3733961	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3733963	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];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];0.97[ASN][1000 genomes]
rs3822652	0.90[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822654	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[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]
rs3892986	1.00[EUR][1000 genomes]
rs57726881	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57749964	1.00[EUR][1000 genomes]
rs58625991	1.00[EUR][1000 genomes]
rs58865195	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59349522	1.00[EUR][1000 genomes]
rs6594652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6864403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6864647	0.82[CHB][hapmap]
rs6891448	0.89[YRI][hapmap]
rs728344	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73227382	1.00[EUR][1000 genomes]
rs73227383	1.00[EUR][1000 genomes]
rs7701868	0.90[ASN][1000 genomes]
rs7706623	0.81[CHD][hapmap]
rs7728109	0.91[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7728481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7728766	0.97[ASN][1000 genomes]
rs7730241	1.00[EUR][1000 genomes]
rs7735121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9687790	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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
rs17135100	REEP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
4	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
6	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
7	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
9	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:112206600-112216400	Weak transcription	Aorta	Aorta
12	chr5:112206600-112217200	Weak transcription	Right Ventricle	heart
13	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:112206800-112215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:112206800-112215800	Weak transcription	Pancreas	Pancrea
17	chr5:112206800-112215800	Weak transcription	Spleen	Spleen
18	chr5:112206800-112217000	Weak transcription	Brain Angular Gyrus	brain
19	chr5:112206800-112217200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:112206800-112217200	Weak transcription	Gastric	stomach
21	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:112206800-112220800	Weak transcription	Ovary	ovary
23	chr5:112207000-112215800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:112207000-112216000	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:112209800-112214800	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:112209800-112218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:112210000-112214800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr5:112210000-112215000	Strong transcription	Primary B cells from cord blood	blood
35	chr5:112210600-112218200	Weak transcription	Psoas Muscle	Psoas
36	chr5:112210600-112225000	Strong transcription	Liver	Liver
37	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:112211000-112214800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:112211200-112216600	Strong transcription	NHDF-Ad	bronchial
41	chr5:112211200-112222600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:112211400-112216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:112211600-112215000	Weak transcription	Fetal Stomach	stomach
45	chr5:112211600-112217200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:112211800-112215200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:112211800-112215200	Weak transcription	Fetal Intestine Small	intestine
49	chr5:112211800-112223400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links