Variant report

Variant	rs13420857
Chromosome Location	chr2:46798005-46798006
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46797930..46799868-chr2:46827992..46829554,2	MCF-7	breast:
2	chr2:46795284..46799480-chr2:46800888..46803285,4	K562	blood:
3	chr2:46796652..46799602-chr2:46801642..46804001,3	MCF-7	breast:
4	chr2:46681213..46683029-chr2:46797843..46800653,2	K562	blood:
5	chr2:46789524..46792081-chr2:46795199..46798160,3	K562	blood:
6	chr2:46770518..46772203-chr2:46796881..46799144,2	K562	blood:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12105801	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12712976	0.81[AMR][1000 genomes]
rs13413254	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451152	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1451153	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1901263	0.80[CHD][hapmap]
rs2305350	0.80[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs3087822	0.80[CHD][hapmap]
rs4384837	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750698	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs13420857	CRIPT	cis	multi-tissue	Pritchard
rs13420857	CRIPT	cis	Frontal Cortex	GTEx
rs13420857	PIGF	cis	multi-tissue	Pritchard
rs13420857	CRIPT	cis	Temporal Cortex	GTEx
rs13420857	PIGF	cis	lymphoblastoid	seeQTL
rs13420857	CRIPT	cis	lymphoblastoid	seeQTL
rs13420857	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13420857	ATP6V1E2	cis	multi-tissue	Pritchard
rs13420857	PIGF	Cis_1M	lymphoblastoid	RTeQTL
rs13420857	CRIPT	cis	parietal	SCAN
rs13420857	RHOQ	cis	cerebellum	SCAN
rs13420857	PIGF	cis	cerebellum	SCAN
rs13420857	CRIPT	cis	Stomach	GTEx
rs13420857	CRIPT	cis	Lymphoblastoid	GTEx
rs13420857	PRKCE	cis	cerebellum	SCAN
rs13420857	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs13420857	PIGF	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46772200-46804000	Weak transcription	NH-A	brain
3	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
5	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:46785400-46798400	Weak transcription	Liver	Liver
13	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
17	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:46787800-46806600	Weak transcription	Gastric	stomach
19	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
20	chr2:46789800-46805800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:46790000-46803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:46790000-46803800	Weak transcription	Primary T cells from cord blood	blood
24	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:46790200-46803400	Weak transcription	A549	lung
27	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:46790600-46803800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:46790600-46806200	Weak transcription	Dnd41	blood
31	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
32	chr2:46793000-46803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:46793000-46806400	Weak transcription	Lung	lung
34	chr2:46793200-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:46793200-46806200	Weak transcription	Aorta	Aorta
36	chr2:46793400-46799800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:46794000-46800200	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:46794400-46799600	Enhancers	Fetal Thymus	thymus
39	chr2:46794600-46800000	Enhancers	Ovary	ovary
40	chr2:46795000-46802400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:46795400-46798200	Flanking Active TSS	GM12878-XiMat	blood
42	chr2:46796000-46800800	Enhancers	Left Ventricle	heart
43	chr2:46796000-46801200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:46796000-46802000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:46796000-46807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:46796200-46799200	Weak transcription	Fetal Intestine Small	intestine
48	chr2:46796200-46800400	Enhancers	Colon Smooth Muscle	Colon
49	chr2:46796200-46806400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:46796200-46807800	Weak transcription	Stomach Mucosa	stomach

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