Variant report

Variant	rs62134736
Chromosome Location	chr2:46766446-46766447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:46766289-46769972	SK-N-SH	brain:	n/a	chr2:46769660-46769673
2	MXI1	chr2:46766247-46772861	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46761516..46767079-chr2:46767675..46771202,5	MCF-7	breast:
2	chr2:46765611..46767976-chr2:47402425..47404067,2	K562	blood:

Variant related genes	Relation type
RHOQ	TF binding region
ENSG00000119729	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1001745	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997164	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13008088	0.87[ASN][1000 genomes]
rs13008418	0.80[AFR][1000 genomes]
rs13008445	0.81[AFR][1000 genomes]
rs13020299	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17817004	0.81[AFR][1000 genomes]
rs34050156	0.93[ASN][1000 genomes]
rs34416415	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35178974	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35870739	0.84[ASN][1000 genomes]
rs4142759	0.87[ASN][1000 genomes]
rs4952831	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952833	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952834	0.93[ASN][1000 genomes]
rs61701220	0.80[AFR][1000 genomes]
rs62134741	0.87[ASN][1000 genomes]
rs6544898	0.81[AFR][1000 genomes]
rs7557190	0.85[AFR][1000 genomes]
rs7607308	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7607633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880671	0.81[AFR][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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3422495	chr2:46761899-46769356	Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs62134736	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs62134736	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs62134736	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs62134736	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs62134736	ATP6V1E2	cis	multi-tissue	Pritchard
rs62134736	ATP6V1E2	cis	Esophagus Mucosa	GTEx
rs62134736	ATP6V1E2	cis	lung	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46747800-46766800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:46748800-46767800	Weak transcription	HSMM	muscle
3	chr2:46748800-46768400	Weak transcription	Ovary	ovary
4	chr2:46753000-46767800	Weak transcription	Placenta	Placenta
5	chr2:46753600-46768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:46755800-46767800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:46756400-46768200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:46756600-46767800	Weak transcription	Pancreas	Pancrea
9	chr2:46760200-46768000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:46760600-46767200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:46760800-46766800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:46760800-46767800	Weak transcription	Fetal Lung	lung
13	chr2:46761000-46767800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:46761200-46767800	Weak transcription	NHEK	skin
15	chr2:46761200-46768600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:46761200-46768800	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:46761400-46768200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:46761600-46768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:46761800-46768400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:46762000-46766600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:46762200-46766800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:46762200-46767600	Weak transcription	K562	blood
23	chr2:46762200-46767800	Weak transcription	Psoas Muscle	Psoas
24	chr2:46762200-46768200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:46762200-46768200	Weak transcription	Aorta	Aorta
26	chr2:46762200-46768200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:46762400-46768400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:46762600-46768200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:46762600-46768600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:46762800-46768400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:46763000-46767200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:46763000-46768000	Enhancers	GM12878-XiMat	blood
33	chr2:46763000-46768200	Weak transcription	Thymus	Thymus
34	chr2:46763000-46768400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:46763000-46768400	Weak transcription	Small Intestine	intestine
36	chr2:46763200-46768000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:46763200-46768600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr2:46763400-46766600	Weak transcription	Right Ventricle	heart
39	chr2:46763400-46766600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:46763400-46766600	Weak transcription	Dnd41	blood
41	chr2:46763400-46767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:46763400-46768000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:46763600-46766800	Weak transcription	A549	lung
44	chr2:46763600-46767000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:46763600-46767000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:46763600-46768000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:46763600-46768600	Weak transcription	Liver	Liver
48	chr2:46764400-46767200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:46764800-46767000	Enhancers	Primary B cells from cord blood	blood
50	chr2:46765000-46766600	Enhancers	Primary hematopoietic stem cells	blood

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