Variant report

Variant	rs1194600
Chromosome Location	chr1:154236009-154236010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154235636-154236083	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:154235976-154236043	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:154235724-154237288	K562	blood:	n/a	n/a
4	POLR2A	chr1:154235276-154236087	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:154235616-154237008	K562	blood:	n/a	n/a
6	POLR2A	chr1:154235461-154237210	K562	blood:	n/a	n/a
7	POLR2A	chr1:154232935-154239560	K562	blood:	n/a	n/a
8	POLR2A	chr1:154235978-154236984	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154193583..154195309-chr1:154234954..154236959,2	K562	blood:
2	chr1:154195648..154197587-chr1:154233739..154236534,2	MCF-7	breast:
3	chr1:154234143..154236997-chr1:154237510..154239479,2	K562	blood:
4	chr1:154166190..154168468-chr1:154235593..154238301,2	K562	blood:
5	chr1:154228115..154231882-chr1:154235436..154238955,4	MCF-7	breast:
6	chr1:154228810..154232286-chr1:154233665..154237376,4	MCF-7	breast:
7	chr1:154189134..154191972-chr1:154235587..154237500,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HAX1-2	chr1:154235977-154236277	NONHSAT006601

No data

Variant related genes	Relation type
UBAP2L	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000201129	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10797058	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10797061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10908751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265285	0.83[EUR][1000 genomes]
rs1194580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194582	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044616	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12095767	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12354278	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13796	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1591902	0.82[CHB][hapmap]
rs2220390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4393149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579747	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845609	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807361	0.85[ASN][1000 genomes]
rs6667222	1.00[JPT][hapmap]
rs6680947	0.80[AMR][1000 genomes]
rs7516809	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7526644	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[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
rs1194600	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	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
5	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:154196800-154242600	Strong transcription	A549	lung
7	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
15	chr1:154197600-154236200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:154197600-154236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:154197600-154239800	Strong transcription	NHLF	lung
22	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
28	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
29	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:154197800-154236400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:154197800-154237200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:154197800-154239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:154197800-154242000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
36	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:154198200-154241000	Strong transcription	Dnd41	blood
40	chr1:154198400-154236600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:154198400-154243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:154198600-154236600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:154200200-154237400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:154205800-154239200	Strong transcription	NHDF-Ad	bronchial
48	chr1:154206200-154236200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
50	chr1:154212000-154237200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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