Variant report

Variant	rs12713498
Chromosome Location	chr2:64112428-64112429
allele	C/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	POLR2A	chr2:64112183-64112554	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:64112249-64114157	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:64112211-64112563	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64110843..64112629-chr2:64128824..64132161,3	MCF-7	breast:
2	chr2:64108206..64110150-chr2:64110899..64112601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251775	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10183479	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11558741	1.00[ASN][1000 genomes]
rs11674020	0.98[ASN][1000 genomes]
rs11676710	0.88[ASN][1000 genomes]
rs11683408	0.92[ASN][1000 genomes]
rs11686956	0.82[ASN][1000 genomes]
rs11691987	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11693906	0.90[ASN][1000 genomes]
rs11694253	0.83[ASN][1000 genomes]
rs11695421	0.92[ASN][1000 genomes]
rs12996866	1.00[ASN][1000 genomes]
rs13018690	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13431781	1.00[ASN][1000 genomes]
rs1440002	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17562177	0.98[ASN][1000 genomes]
rs17562423	0.90[ASN][1000 genomes]
rs17619753	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs193031	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2302808	0.98[ASN][1000 genomes]
rs2439183	0.88[ASN][1000 genomes]
rs2969395	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329478	0.88[ASN][1000 genomes]
rs329488	0.80[ASN][1000 genomes]
rs34122334	0.96[ASN][1000 genomes]
rs34765999	0.88[ASN][1000 genomes]
rs34777730	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs35002211	0.98[ASN][1000 genomes]
rs35336851	0.83[ASN][1000 genomes]
rs35474183	0.88[ASN][1000 genomes]
rs35480874	0.88[ASN][1000 genomes]
rs35697586	0.88[ASN][1000 genomes]
rs35960986	0.82[ASN][1000 genomes]
rs36033991	0.98[ASN][1000 genomes]
rs36123537	0.90[ASN][1000 genomes]
rs4233930	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4538187	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4671071	0.94[ASN][1000 genomes]
rs4671073	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs56904032	0.92[ASN][1000 genomes]
rs6546029	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6546030	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6546032	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6546033	0.98[ASN][1000 genomes]
rs6546035	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs66980330	1.00[ASN][1000 genomes]
rs6710763	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67308158	1.00[ASN][1000 genomes]
rs6731508	1.00[ASN][1000 genomes]
rs6732746	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6755646	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67615384	0.96[ASN][1000 genomes]
rs67765474	0.98[ASN][1000 genomes]
rs68117986	0.92[ASN][1000 genomes]
rs72808243	0.96[ASN][1000 genomes]
rs72893103	0.92[ASN][1000 genomes]
rs7590399	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12713498	UGP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:64101200-64113600	Weak transcription	Fetal Stomach	stomach
4	chr2:64101800-64112800	Weak transcription	Fetal Kidney	kidney
5	chr2:64102200-64113000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:64103200-64117400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:64103600-64118600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:64103600-64128400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:64103800-64130400	Weak transcription	Stomach Mucosa	stomach
10	chr2:64104000-64113400	Weak transcription	Brain Substantia Nigra	brain
11	chr2:64104000-64113600	Weak transcription	Fetal Brain Male	brain
12	chr2:64105200-64121600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:64105600-64118400	Strong transcription	HepG2	liver
14	chr2:64107200-64130000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:64107400-64116400	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:64107400-64119000	Strong transcription	HSMMtube	muscle
17	chr2:64107400-64119200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:64107400-64121400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:64107400-64121800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:64107400-64127600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:64107400-64129600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:64107600-64122000	Strong transcription	HSMM	muscle
23	chr2:64107600-64122200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:64107600-64122200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:64107600-64122200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr2:64107600-64128800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:64107600-64129200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:64107800-64112600	Strong transcription	Colonic Mucosa	Colon
29	chr2:64107800-64115800	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:64107800-64117600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:64107800-64118800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:64107800-64124600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:64107800-64126200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:64107800-64127000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:64108000-64113400	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr2:64108000-64118600	Strong transcription	A549	lung
37	chr2:64108200-64113400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:64108200-64115600	Strong transcription	Liver	Liver
39	chr2:64108200-64120800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:64108200-64121800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:64108200-64127200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:64108400-64121400	Strong transcription	HMEC	breast
43	chr2:64108400-64127200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:64108600-64113200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:64108600-64115600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr2:64108600-64128200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:64108800-64121400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:64108800-64121400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:64108800-64121800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:64109000-64113800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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