Variant report

Variant	rs12531518
Chromosome Location	chr7:27661139-27661140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10081338	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10081339	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1015265	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1030003	0.81[AMR][1000 genomes]
rs10447552	0.86[AMR][1000 genomes]
rs10486548	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10951173	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1115346	0.81[EUR][1000 genomes]
rs11762342	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11763449	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11764753	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11973492	0.82[AMR][1000 genomes]
rs12155430	0.86[AMR][1000 genomes]
rs12530626	0.82[AMR][1000 genomes]
rs12535844	0.85[AMR][1000 genomes]
rs12540063	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665991	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12667610	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12668430	0.81[AMR][1000 genomes]
rs12670771	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12672811	0.86[AMR][1000 genomes]
rs12673949	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700822	0.81[AMR][1000 genomes]
rs12700823	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700824	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700825	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700828	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12700829	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700830	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13226102	0.81[AMR][1000 genomes]
rs13242248	0.86[AMR][1000 genomes]
rs13244903	0.86[AMR][1000 genomes]
rs13246464	0.85[AMR][1000 genomes]
rs13308974	0.81[AMR][1000 genomes]
rs1404282	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1524529	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1608663	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980330	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2041715	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2110528	0.81[AMR][1000 genomes]
rs2160125	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391444	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2391445	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2391446	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2391447	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391448	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391449	0.81[AMR][1000 genomes]
rs2391451	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391452	0.86[AMR][1000 genomes]
rs2391453	0.86[AMR][1000 genomes]
rs2391454	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28416309	0.82[AMR][1000 genomes]
rs42085	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs42087	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs42088	0.89[AFR][1000 genomes]
rs42092	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs42098	0.89[AFR][1000 genomes]
rs4722724	0.81[AMR][1000 genomes]
rs4722726	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4722728	0.86[AMR][1000 genomes]
rs56139857	0.82[AMR][1000 genomes]
rs6462033	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6462036	0.81[AMR][1000 genomes]
rs6462038	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462039	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6943883	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6945993	0.82[AMR][1000 genomes]
rs6946305	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6948460	0.86[AMR][1000 genomes]
rs6948814	0.81[AMR][1000 genomes]
rs6954905	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6957378	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6959495	0.86[AMR][1000 genomes]
rs6963421	0.85[AMR][1000 genomes]
rs6966091	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6966587	0.86[AMR][1000 genomes]
rs6970104	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6974387	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6974932	0.89[AMR][1000 genomes]
rs759270	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs759271	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7779990	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7782422	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7786973	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7790498	0.88[AMR][1000 genomes]
rs7806415	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7806812	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7808275	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7811436	0.81[AMR][1000 genomes]
rs961723	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs961724	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs961725	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639559	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs974883	0.86[AMR][1000 genomes];0.83[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv1802647	chr7:27658495-27673924	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12531518	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12531518	HIBADH	cis	multi-tissue	Pritchard
rs12531518	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
2	chr7:27654400-27696400	Weak transcription	Gastric	stomach
3	chr7:27655400-27665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:27657200-27662200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:27657400-27661800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:27657400-27661800	ZNF genes & repeats	Fetal Intestine Large	intestine
7	chr7:27657400-27662600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr7:27658000-27661400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr7:27658200-27661200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:27658200-27661400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
11	chr7:27658400-27661200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr7:27658400-27661200	ZNF genes & repeats	Fetal Lung	lung
13	chr7:27658400-27661400	ZNF genes & repeats	Liver	Liver
14	chr7:27658400-27662000	ZNF genes & repeats	Dnd41	blood
15	chr7:27658600-27661200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:27658600-27661200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:27659200-27661200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr7:27659600-27661400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr7:27659800-27661600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:27659800-27672800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:27659800-27675400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:27659800-27679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:27660000-27661200	Weak transcription	Aorta	Aorta
26	chr7:27660000-27661200	Weak transcription	Lung	lung
27	chr7:27660000-27664400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:27660000-27667600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:27660000-27669800	Weak transcription	Left Ventricle	heart
30	chr7:27660000-27680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:27660200-27661800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr7:27660200-27668000	Weak transcription	Osteobl	bone
33	chr7:27660200-27674600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr7:27660400-27668600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:27660400-27675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:27660400-27680200	Weak transcription	Fetal Kidney	kidney
37	chr7:27660600-27666600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:27660600-27667800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:27660600-27674800	Weak transcription	Psoas Muscle	Psoas
40	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
41	chr7:27660800-27661800	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr7:27660800-27661800	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr7:27660800-27668400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:27660800-27675600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:27660800-27676400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:27661000-27661200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:27661000-27661400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr7:27661000-27661400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:27661000-27661800	ZNF genes & repeats	Fetal Stomach	stomach
50	chr7:27661000-27661800	Strong transcription	Ovary	ovary

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