Variant report

Variant	rs34921640
Chromosome Location	chr15:43721385-43721386
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43713407..43715929-chr15:43720656..43722295,2	K562	blood:
2	chr15:43720819..43722875-chr15:43725528..43727574,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10518812	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12899865	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12900259	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12905220	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12906017	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12906481	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12907870	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12908460	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12911569	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12911740	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12913977	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12914122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16957680	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957715	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957730	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17723479	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17780417	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17780920	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1814324	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2230451	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34002293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34178146	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34181131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34212866	0.85[EUR][1000 genomes]
rs34388946	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34515241	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34591748	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34633582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34657657	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34661349	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34697113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34767197	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34860428	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35158584	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35160541	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35278805	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35311230	0.84[AFR][1000 genomes]
rs35326382	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35681736	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35903301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35958032	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35975365	0.82[EUR][1000 genomes]
rs35992154	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36078097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3862138	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs514438	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55748552	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55801120	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57728767	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57938858	0.83[EUR][1000 genomes]
rs60018990	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60367691	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62019432	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62020574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020575	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62020612	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62020616	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62021176	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62021180	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66629206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71476435	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7168220	0.81[EUR][1000 genomes]
rs7173383	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7176923	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7177146	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7177892	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7180812	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7181545	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7181634	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181783	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7182292	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7183708	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72707530	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72709850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72709879	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8027748	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34921640	TUBGCP4	cis	Artery Tibial	GTEx
rs34921640	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs34921640	ZSCAN29	cis	multi-tissue	Pritchard
rs34921640	LCMT2	cis	Esophagus Mucosa	GTEx
rs34921640	TGM7	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:43682800-43727800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:43683400-43732200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:43686000-43727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:43686600-43726000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:43686600-43733200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:43686600-43733800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:43686800-43725400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:43686800-43725600	Strong transcription	Osteobl	bone
12	chr15:43686800-43733400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:43687000-43725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:43687000-43732200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:43687200-43733400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:43687600-43731600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:43689200-43737200	Weak transcription	Stomach Mucosa	stomach
18	chr15:43700000-43748400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:43703200-43739800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:43703600-43731400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:43703800-43724800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:43704200-43727200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:43709200-43724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:43709400-43741600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:43709800-43723600	Weak transcription	Fetal Brain Male	brain
26	chr15:43711400-43726400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:43711600-43723000	Weak transcription	Psoas Muscle	Psoas
28	chr15:43713200-43729600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr15:43713600-43750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:43713800-43722000	Weak transcription	Fetal Heart	heart
31	chr15:43714000-43748200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:43714400-43723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:43714400-43724200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:43714400-43724200	Weak transcription	Small Intestine	intestine
35	chr15:43714400-43724400	Weak transcription	HMEC	breast
36	chr15:43714400-43733000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr15:43715000-43722800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:43715000-43723800	Weak transcription	NHLF	lung
39	chr15:43715000-43747600	Weak transcription	Right Ventricle	heart
40	chr15:43715200-43723200	Weak transcription	Pancreas	Pancrea
41	chr15:43715400-43724400	Weak transcription	Spleen	Spleen
42	chr15:43715600-43748200	Weak transcription	Colonic Mucosa	Colon
43	chr15:43715800-43723800	Weak transcription	HepG2	liver
44	chr15:43715800-43724400	Weak transcription	Lung	lung
45	chr15:43716800-43722000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:43717000-43722800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:43718000-43723000	Weak transcription	Colon Smooth Muscle	Colon
48	chr15:43718400-43727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:43719200-43725000	Strong transcription	NH-A	brain
50	chr15:43719200-43725800	Strong transcription	HSMM	muscle

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