Variant report

Variant	rs3790613
Chromosome Location	chr1:154210671-154210672
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:154209716-154210777	HepG2	liver:	n/a	n/a
2	CEBPB	chr1:154210601-154210900	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

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	chr1:154207955..154211164-chr1:154212760..154216262,4	MCF-7	breast:
4	chr1:154153510..154155869-chr1:154207708..154210677,2	MCF-7	breast:
5	chr1:154208334..154210712-chr1:154220041..154222469,3	MCF-7	breast:
6	chr1:154201106..154203777-chr1:154208596..154211363,2	K562	blood:
7	chr1:154209373..154211849-chr1:154214805..154217325,2	K562	blood:
8	chr1:154192348..154196055-chr1:154207328..154211184,7	MCF-7	breast:
9	chr1:154199628..154201203-chr1:154208732..154211600,2	MCF-7	breast:
10	chr1:154202277..154205016-chr1:154208534..154211363,2	K562	blood:

No data

Variant related genes	Relation type
UBAP2L	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10158820	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1044013	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265238	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11265251	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11802893	0.82[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs1194593	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194596	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12023901	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12025237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026177	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs12026615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12028554	0.86[ASN][1000 genomes]
rs12028949	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs12043131	0.91[CEU][hapmap];0.83[AFR][1000 genomes]
rs12062977	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12135346	0.88[ASN][1000 genomes]
rs12733060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742691	0.87[ASN][1000 genomes]
rs12743874	0.89[ASN][1000 genomes]
rs12749447	0.88[ASN][1000 genomes]
rs12750321	0.89[ASN][1000 genomes]
rs16835846	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs16835852	0.87[JPT][hapmap]
rs1760801	0.82[ASN][1000 genomes]
rs1760802	0.95[JPT][hapmap]
rs1986709	0.85[ASN][1000 genomes]
rs2274993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282227	0.96[ASN][1000 genomes]
rs2340473	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2790689	0.82[JPT][hapmap]
rs28372838	0.80[EUR][1000 genomes]
rs2879788	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs34128679	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34335016	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34752019	0.82[JPT][hapmap]
rs35761479	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3762339	0.87[ASN][1000 genomes]
rs3762340	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3790614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811453	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3811455	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs3828077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935419	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4240871	0.86[ASN][1000 genomes]
rs4459102	0.82[JPT][hapmap]
rs4620534	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs6427509	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6657214	0.86[ASN][1000 genomes]
rs6671009	0.82[JPT][hapmap]
rs6673752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676022	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6719	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7517578	0.84[ASN][1000 genomes]
rs9803857	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9943093	0.87[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195200-154211400	Weak transcription	Right Atrium	heart
2	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:154196400-154218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
8	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:154196800-154211800	Strong transcription	NHEK	skin
10	chr1:154196800-154224200	Strong transcription	K562	blood
11	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
12	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
13	chr1:154196800-154242600	Strong transcription	A549	lung
14	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:154197200-154210800	Strong transcription	HMEC	breast
21	chr1:154197200-154214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:154197400-154212200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
26	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
27	chr1:154197600-154211200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:154197600-154211200	Strong transcription	Lung	lung
29	chr1:154197600-154212800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:154197600-154213200	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr1:154197600-154214000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:154197600-154214600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:154197600-154218600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:154197600-154218800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:154197600-154226400	Strong transcription	Osteobl	bone
36	chr1:154197600-154236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:154197600-154236200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:154197600-154236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:154197600-154239800	Strong transcription	NHLF	lung
44	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
50	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose

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