Variant report

Variant	rs7565274
Chromosome Location	chr2:46841861-46841862
allele	G/T
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	MEF2A	chr2:46841841-46842237	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46839258..46842242-chr2:46842497..46844194,2	K562	blood:
2	chr2:46694377..46696235-chr2:46839785..46842336,2	MCF-7	breast:
3	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:

Variant related genes	Relation type
PIGF	TF binding region
CRIPT	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13024534	0.95[ASN][1000 genomes]
rs13032670	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13033177	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1378764	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767994	0.95[ASN][1000 genomes]
rs17768018	0.95[ASN][1000 genomes]
rs17768132	0.95[ASN][1000 genomes]
rs17768138	0.91[ASN][1000 genomes]
rs17768226	0.82[ASN][1000 genomes]
rs17818399	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819022	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1824050	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122715	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346419	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34449783	0.95[ASN][1000 genomes]
rs34544165	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34748737	0.95[ASN][1000 genomes]
rs34752561	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996358	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35350086	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35449212	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35682608	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35837037	0.95[ASN][1000 genomes]
rs35949012	0.95[ASN][1000 genomes]
rs4952836	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4952837	0.95[ASN][1000 genomes]
rs55742873	0.82[ASN][1000 genomes]
rs62136864	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62136873	0.95[ASN][1000 genomes]
rs62136894	0.91[ASN][1000 genomes]
rs6746598	0.95[ASN][1000 genomes]
rs7590693	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs896212	0.91[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	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	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
4	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
5	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
6	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
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7565274	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs7565274	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs7565274	CRIPT	cis	multi-tissue	Pritchard
rs7565274	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:46802400-46842600	Weak transcription	NHEK	skin
4	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:46807800-46842400	Weak transcription	NHLF	lung
8	chr2:46807800-46842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:46807800-46842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:46807800-46842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:46807800-46842800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:46807800-46842800	Weak transcription	HSMMtube	muscle
13	chr2:46807800-46843000	Weak transcription	Brain Germinal Matrix	brain
14	chr2:46807800-46843000	Weak transcription	Fetal Stomach	stomach
15	chr2:46807800-46843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:46808000-46842800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:46808600-46842800	Weak transcription	Placenta	Placenta
18	chr2:46809400-46842800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:46809600-46842800	Weak transcription	Fetal Thymus	thymus
20	chr2:46810600-46842600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:46811600-46842800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:46811800-46842400	Weak transcription	Osteobl	bone
23	chr2:46811800-46843000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:46812000-46842600	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:46819600-46842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:46819800-46842200	Weak transcription	NHDF-Ad	bronchial
27	chr2:46824200-46842800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:46828000-46842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:46828600-46842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:46828600-46842800	Weak transcription	Left Ventricle	heart
31	chr2:46829000-46842800	Weak transcription	Brain Angular Gyrus	brain
32	chr2:46829200-46842600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:46829800-46843200	Weak transcription	Ovary	ovary
34	chr2:46830800-46842400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:46831600-46842800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:46833600-46843200	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:46834200-46842600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:46834200-46842800	Weak transcription	Liver	Liver
39	chr2:46834600-46842800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:46834600-46842800	Weak transcription	Right Ventricle	heart
41	chr2:46835200-46842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:46835400-46842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:46835800-46843000	Weak transcription	Fetal Brain Male	brain
44	chr2:46836400-46842400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:46836600-46842200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:46836600-46842200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:46836600-46842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:46836600-46842800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:46836600-46842800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:46836800-46842800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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