Variant report

Variant	rs12477310
Chromosome Location	chr2:64370586-64370587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64245248..64247097-chr2:64369855..64371570,2	MCF-7	breast:
2	chr2:64368361..64371459-chr2:64452988..64456076,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS54-4	chr2:64370452-64370660	NONHSAT071090

Variant related genes	Relation type
ENSG00000225889	Chromatin interaction
ENSG00000143952	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10496107	0.82[JPT][hapmap]
rs12151701	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12472816	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs12479211	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12988261	0.83[ASN][1000 genomes]
rs34283299	0.83[ASN][1000 genomes]
rs6730262	0.82[JPT][hapmap]
rs6733160	0.82[JPT][hapmap]
rs72810209	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72810212	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72810213	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72810219	0.88[ASN][1000 genomes]
rs7349403	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs7573532	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	esv3373290	chr2:64370073-64372621	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477310	UGP2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64365400-64370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:64366400-64371800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr2:64366800-64371200	Active TSS	Right Atrium	heart
4	chr2:64367000-64370600	Weak transcription	Gastric	stomach
5	chr2:64367200-64372400	Active TSS	GM12878-XiMat	blood
6	chr2:64368200-64371800	Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr2:64368200-64372000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:64368600-64370600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:64368600-64370600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:64368600-64371600	Active TSS	Fetal Muscle Leg	muscle
11	chr2:64368600-64371800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:64368600-64372000	Active TSS	Brain Angular Gyrus	brain
13	chr2:64368800-64370600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:64368800-64370600	Flanking Active TSS	Dnd41	blood
15	chr2:64368800-64371800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:64368800-64371800	Active TSS	Thymus	Thymus
17	chr2:64368800-64372000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:64368800-64372000	Active TSS	Right Ventricle	heart
19	chr2:64368800-64372200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:64369000-64370600	Weak transcription	Spleen	Spleen
21	chr2:64369000-64370800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:64369000-64371600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:64369000-64371600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:64369000-64371600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:64369000-64371600	Active TSS	Primary T cells fromperipheralblood	blood
26	chr2:64369000-64371800	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr2:64369000-64371800	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:64369000-64371800	Active TSS	NHDF-Ad	bronchial
29	chr2:64369000-64372000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:64369000-64372000	Active TSS	Aorta	Aorta
31	chr2:64369000-64372000	Active TSS	Colonic Mucosa	Colon
32	chr2:64369000-64372000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr2:64369000-64372000	Active TSS	Fetal Intestine Small	intestine
34	chr2:64369000-64372000	Active TSS	Fetal Stomach	stomach
35	chr2:64369000-64372000	Active TSS	Psoas Muscle	Psoas
36	chr2:64369000-64372000	Active TSS	Rectal Smooth Muscle	rectum
37	chr2:64369000-64372000	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:64369000-64372000	Active TSS	NHLF	lung
39	chr2:64369000-64372200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:64369000-64372200	Active TSS	Duodenum Mucosa	Duodenum
41	chr2:64369200-64370600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr2:64369200-64371200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr2:64369200-64371600	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr2:64369200-64371600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:64369200-64371600	Active TSS	Fetal Thymus	thymus
46	chr2:64369200-64371600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr2:64369200-64371800	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr2:64369200-64371800	Active TSS	Brain Anterior Caudate	brain
49	chr2:64369200-64371800	Active TSS	Brain Cingulate Gyrus	brain
50	chr2:64369200-64371800	Active TSS	Brain Hippocampus Middle	brain

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