Variant report

Variant	rs2346419
Chromosome Location	chr2:46845069-46845070
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:46845066-46845287	HepG2	liver:	n/a	chr2:46845134-46845151
2	POLR2A	chr2:46843137-46845416	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr2:46842494-46845378	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:46842777-46845152	PBDE	blood:	n/a	n/a
5	SIN3A	chr2:46843161-46845213	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr2:46845035-46845348	K562	blood:	n/a	chr2:46845134-46845151

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46691583..46692300-chr2:46844576..46845112,2	MCF-7	breast:
2	chr17:4612398..4613899-chr2:46843451..46845435,2	MCF-7	breast:
3	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
4	chr2:46843200..46845178-chr2:47140240..47142665,2	MCF-7	breast:
5	chr2:46844525..46846523-chr2:46850500..46852298,2	MCF-7	breast:
6	chr2:46844343..46845232-chr3:52719605..52720531,2	NB4	blood:
7	chr2:46806489..46808552-chr2:46842875..46845193,2	MCF-7	breast:
8	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
9	chr2:46788951..46790463-chr2:46844313..46846805,2	K562	blood:
10	chr2:46811229..46813597-chr2:46844623..46846343,2	K562	blood:

No data

Variant related genes	Relation type
PIGF	TF binding region
ENSG00000119729	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000141480	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000250116	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10495934	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12105006	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13032670	0.80[EUR][1000 genomes]
rs13033177	0.80[EUR][1000 genomes]
rs1378764	0.81[EUR][1000 genomes]
rs17818399	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1824050	0.81[EUR][1000 genomes]
rs2122715	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34544165	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34752561	0.82[EUR][1000 genomes]
rs34996358	0.84[EUR][1000 genomes]
rs35350086	0.81[EUR][1000 genomes]
rs35449212	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35682608	0.82[EUR][1000 genomes]
rs4952836	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62136864	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6544909	0.90[CHB][hapmap]
rs7560464	0.91[CHB][hapmap]
rs7565274	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7590693	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs982395	1.00[CHB][hapmap];0.81[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2346419	ATP6V1E2	cis	Skin Sun Exposed Lower leg	GTEx
rs2346419	CRIPT	cis	multi-tissue	Pritchard
rs2346419	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs2346419	CRIPT	cis	Temporal Cortex	GTEx
rs2346419	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs2346419	CRIPT	cis	Frontal Cortex	GTEx
rs2346419	CRIPT	cis	Lymphoblastoid	GTEx
rs2346419	ATP6V1E2	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46842600-46845400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:46842600-46845600	Active TSS	Aorta	Aorta
3	chr2:46842800-46845200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:46842800-46845200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:46842800-46845400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:46842800-46845400	Active TSS	Right Atrium	heart
7	chr2:46843000-46845200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:46843000-46845200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:46843000-46845200	Active TSS	Fetal Intestine Small	intestine
10	chr2:46843000-46845200	Active TSS	GM12878-XiMat	blood
11	chr2:46843000-46845400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:46843000-46845400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:46843000-46845400	Active TSS	Psoas Muscle	Psoas
14	chr2:46843000-46845400	Active TSS	K562	blood
15	chr2:46843000-46845600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr2:46843000-46845600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr2:46843200-46845200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:46843200-46845200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:46843200-46845200	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr2:46843200-46845200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:46843200-46845200	Active TSS	Ovary	ovary
22	chr2:46843400-46845200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:46843400-46845400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:46843600-46845200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:46843600-46845200	Active TSS	Colonic Mucosa	Colon
26	chr2:46843600-46845200	Active TSS	Fetal Muscle Trunk	muscle
27	chr2:46843600-46845200	Active TSS	Stomach Smooth Muscle	stomach
28	chr2:46843600-46845200	Active TSS	HSMMtube	muscle
29	chr2:46843600-46845400	Active TSS	Fetal Thymus	thymus
30	chr2:46843600-46845400	Active TSS	NH-A	brain
31	chr2:46844200-46845200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:46844400-46845200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr2:46844400-46845400	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr2:46844400-46845400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr2:46844400-46845600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:46844400-46845800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:46844600-46845200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr2:46844600-46845200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:46844600-46845200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:46844600-46845200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:46844600-46845200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:46844600-46845200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr2:46844600-46845400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:46844600-46845400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr2:46844600-46845400	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr2:46844600-46845400	Flanking Active TSS	Liver	Liver
47	chr2:46844600-46845400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr2:46844600-46845400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:46844600-46845400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr2:46844600-46845400	Flanking Active TSS	HUVEC	blood vessel

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