Variant report

Variant	rs12062977
Chromosome Location	chr1:154211516-154211517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154210658..154214803-chr1:154216327..154221110,6	K562	blood:
2	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
3	chr1:154206043..154208545-chr1:154210918..154213317,2	K562	blood:
4	chr1:154209373..154211849-chr1:154214805..154217325,2	K562	blood:
5	chr1:154199628..154201203-chr1:154208732..154211600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10158820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044013	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10797047	0.90[ASN][1000 genomes]
rs11265238	0.91[JPT][hapmap]
rs11265251	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265425	0.95[JPT][hapmap]
rs11802893	0.82[JPT][hapmap]
rs1194593	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1194596	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12023901	0.86[ASN][1000 genomes]
rs12025237	0.96[JPT][hapmap];0.87[ASN][1000 genomes]
rs12026177	0.91[JPT][hapmap]
rs12026615	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12027999	0.87[ASN][1000 genomes]
rs12028554	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12028949	0.91[JPT][hapmap]
rs12029331	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12733060	0.87[ASN][1000 genomes]
rs12738393	0.87[ASN][1000 genomes]
rs16835846	0.87[JPT][hapmap]
rs16835852	0.84[JPT][hapmap]
rs1760802	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs1760803	0.83[ASN][1000 genomes]
rs1986709	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274993	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2282227	0.84[ASN][1000 genomes]
rs2340473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762340	0.96[JPT][hapmap];0.84[ASN][1000 genomes]
rs3790613	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3790614	0.87[ASN][1000 genomes]
rs3811453	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3811455	0.91[JPT][hapmap]
rs3828076	0.82[EUR][1000 genomes]
rs3828077	0.96[JPT][hapmap];0.87[ASN][1000 genomes]
rs3935419	0.91[JPT][hapmap]
rs4240871	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4620534	0.91[JPT][hapmap]
rs6427509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657214	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667222	0.84[YRI][hapmap]
rs6673752	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517578	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524346	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9803857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats 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	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12062977	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:154196400-154218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
7	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:154196800-154211800	Strong transcription	NHEK	skin
9	chr1:154196800-154224200	Strong transcription	K562	blood
10	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
11	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
12	chr1:154196800-154242600	Strong transcription	A549	lung
13	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:154197200-154214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:154197400-154212200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
24	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
25	chr1:154197600-154212800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:154197600-154213200	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:154197600-154214000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:154197600-154214600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:154197600-154218600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:154197600-154218800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:154197600-154226400	Strong transcription	Osteobl	bone
32	chr1:154197600-154236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:154197600-154236200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:154197600-154236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:154197600-154239800	Strong transcription	NHLF	lung
40	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
46	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:154197800-154220400	Strong transcription	Primary T cells from cord blood	blood
49	chr1:154197800-154236400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:154197800-154237200	Strong transcription	Primary monocytes fromperipheralblood	blood

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