Variant report

Variant	rs12188270
Chromosome Location	chr5:68575265-68575266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10805428	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1134774	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11739602	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12520485	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13161541	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13163459	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178023	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13182409	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1976101	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054975	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054976	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2130756	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172055	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327638	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327639	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932785	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932787	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932788	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932789	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932790	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932793	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972357	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972364	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972367	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972369	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972379	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972384	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972385	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34261117	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34449359	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34591347	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34657177	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350092	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350096	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350118	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350121	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4367248	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423955	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668139	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6865178	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71622283	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706902	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711657	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12188270	RAD17	cis	Muscle Skeletal	GTEx
rs12188270	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
5	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:68549400-68577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:68549600-68577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:68550600-68577000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:68553000-68581400	Weak transcription	Psoas Muscle	Psoas
14	chr5:68553800-68575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
16	chr5:68554000-68577600	Weak transcription	Fetal Heart	heart
17	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:68557200-68575400	Weak transcription	Gastric	stomach
19	chr5:68557400-68575400	Weak transcription	Right Ventricle	heart
20	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:68559200-68581200	Weak transcription	Fetal Kidney	kidney
22	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:68560400-68575400	Weak transcription	HSMMtube	muscle
24	chr5:68562000-68576400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:68562400-68577000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:68562600-68578800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:68562800-68577400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:68563000-68585200	Strong transcription	Liver	Liver
30	chr5:68563200-68577400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:68563400-68576000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:68564200-68575400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr5:68564200-68575400	Weak transcription	Esophagus	oesophagus
34	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
35	chr5:68564400-68575400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:68566600-68575400	Weak transcription	Brain Angular Gyrus	brain
39	chr5:68566600-68575800	Weak transcription	Brain Substantia Nigra	brain
40	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:68567400-68575400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:68567800-68575400	Weak transcription	K562	blood
43	chr5:68567800-68578200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:68569000-68576400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:68569200-68576400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:68569400-68582000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:68569600-68575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:68569800-68575400	Weak transcription	A549	lung
49	chr5:68569800-68576800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr5:68570200-68575400	Weak transcription	Stomach Smooth Muscle	stomach

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