Variant report

Variant	rs2122715
Chromosome Location	chr2:46845849-46845850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46845368..46847323-chr2:47016580..47018230,2	K562	blood:
2	chr2:46845600..46848148-chr2:46860947..46862599,2	K562	blood:
3	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
4	chr2:46844525..46846523-chr2:46850500..46852298,2	MCF-7	breast:
5	chr2:46845764..46848148-chr2:46860387..46862849,3	K562	blood:
6	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
7	chr2:46788951..46790463-chr2:46844313..46846805,2	K562	blood:
8	chr2:46811229..46813597-chr2:46844623..46846343,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13000706	0.86[CHD][hapmap]
rs13013245	1.00[JPT][hapmap]
rs13024534	0.95[ASN][1000 genomes]
rs13032670	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13033177	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1378764	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451156	0.82[CHD][hapmap]
rs1531133	0.86[CHD][hapmap]
rs17767994	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17768018	0.95[ASN][1000 genomes]
rs17768132	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17768138	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17768226	0.82[ASN][1000 genomes]
rs17818399	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17819022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1824050	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346419	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3087822	0.80[CHD][hapmap]
rs34449783	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34544165	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34748737	0.95[ASN][1000 genomes]
rs34752561	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996358	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35350086	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35449212	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35682608	0.91[AMR][1000 genomes];0.89[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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4952837	0.95[ASN][1000 genomes]
rs55742873	0.82[ASN][1000 genomes]
rs62136864	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62136873	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62136894	0.91[ASN][1000 genomes]
rs6746598	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7565274	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590693	0.89[AMR][1000 genomes];0.96[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2122715	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs2122715	CRIPT	cis	multi-tissue	Pritchard
rs2122715	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs2122715	CRIPT	cis	parietal	SCAN
rs2122715	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs2122715	ATP6V1E2	cis	parietal	SCAN
rs2122715	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs2122715	PIGF	cis	cerebellum	SCAN
rs2122715	PIGF	cis	parietal	SCAN
rs2122715	PIGF	cis	lymphoblastoid	seeQTL
rs2122715	CRIPT	cis	lymphoblastoid	seeQTL
rs2122715	CRIPT	cis	Temporal Cortex	GTEx
rs2122715	CRIPT	cis	Frontal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844600-46847200	Weak transcription	Spleen	Spleen
2	chr2:46844800-46846000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr2:46844800-46847200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46844800-46847200	Weak transcription	Lung	lung
5	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
9	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
10	chr2:46845000-46846000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:46845000-46846000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:46845000-46846400	Weak transcription	Placenta	Placenta
13	chr2:46845000-46847000	Weak transcription	Left Ventricle	heart
14	chr2:46845200-46846000	Enhancers	Primary B cells from cord blood	blood
15	chr2:46845200-46846000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:46845200-46846000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:46845200-46846000	Enhancers	HSMM	muscle
18	chr2:46845200-46846200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:46845200-46846200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:46845200-46846200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:46845200-46846200	Enhancers	Colon Smooth Muscle	Colon
22	chr2:46845200-46846800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:46845200-46846800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:46845200-46846800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:46845200-46846800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:46845200-46846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:46845200-46847000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:46845200-46847200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:46845200-46847200	Weak transcription	Gastric	stomach
30	chr2:46845200-46847200	Weak transcription	Ovary	ovary
31	chr2:46845200-46847400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:46845200-46847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:46845200-46850000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:46845200-46854000	Weak transcription	Colonic Mucosa	Colon
35	chr2:46845400-46846000	Enhancers	Primary T cells from cord blood	blood
36	chr2:46845400-46846000	Enhancers	Adipose Nuclei	Adipose
37	chr2:46845400-46846000	Enhancers	Liver	Liver
38	chr2:46845400-46846000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:46845400-46846000	Enhancers	Duodenum Mucosa	Duodenum
40	chr2:46845400-46846000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:46845400-46846000	Enhancers	Fetal Intestine Small	intestine
42	chr2:46845400-46846000	Enhancers	Rectal Smooth Muscle	rectum
43	chr2:46845400-46846000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:46845400-46846000	Enhancers	Stomach Smooth Muscle	stomach
45	chr2:46845400-46846000	Enhancers	HepG2	liver
46	chr2:46845400-46846200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:46845400-46846400	Enhancers	Hela-S3	cervix
48	chr2:46845400-46846800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:46845400-46846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:46845400-46846800	Weak transcription	Fetal Intestine Large	intestine

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