Variant report

Variant	rs3789460
Chromosome Location	chr1:94339844-94339845
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:194)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:194 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:94339588-94339884	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:94339700-94339850	HFF-Myc	foreskin:	n/a	n/a
3	CTCF	chr1:94339800-94339950	BE2_C	brain:	n/a	n/a
4	SMC3	chr1:94339635-94339889	K562	blood:	n/a	n/a
5	CTCF	chr1:94339800-94339950	K562	blood:	n/a	n/a
6	CTCF	chr1:94339733-94339871	GM12892	blood:	n/a	n/a
7	CTCF	chr1:94339720-94339870	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr1:94339707-94339924	Medullo	brain:	n/a	n/a
9	CTCF	chr1:94339740-94339890	A549	lung:	n/a	n/a
10	RAD21	chr1:94339526-94340064	A549	lung:	n/a	n/a
11	POLR2A	chr1:94339709-94339942	K562	blood:	n/a	n/a
12	CTCF	chr1:94339820-94339970	HVMF	connective:	n/a	n/a
13	POLR2A	chr1:94339555-94340282	A549	lung:	n/a	n/a
14	CTCF	chr1:94339740-94339890	HCM	heart:	n/a	n/a
15	FOS	chr1:94339697-94339844	MCF10A-Er-Src	breast:	n/a	chr1:94339701-94339712
16	CTCF	chr1:94339677-94339936	A549	lung:	n/a	n/a
17	RFX5	chr1:94339691-94339983	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr1:94339740-94339890	HCT-116	colon:	n/a	n/a
19	CTCF	chr1:94339700-94339850	NHEK	skin:	n/a	n/a
20	POLR2A	chr1:94333938-94341380	K562	blood:	n/a	n/a
21	CTCF	chr1:94339740-94339890	RPTEC	kidney:	n/a	n/a
22	CTCF	chr1:94339780-94339930	HFF	foreskin:	n/a	n/a
23	CTCF	chr1:94339740-94339890	NHDF-neo	bronchial:	n/a	n/a
24	CTCF	chr1:94339683-94339962	HUVEC	blood vessel:	n/a	n/a
25	SMC3	chr1:94339633-94339930	GM12878	blood:	n/a	n/a
26	CTCF	chr1:94339722-94339942	Spleen_OC	spleen:	n/a	n/a
27	CTCF	chr1:94339720-94339870	HVMF	connective:	n/a	n/a
28	SMC3	chr1:94339618-94339984	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr1:94339720-94339870	GM12872	blood:	n/a	n/a
30	CTCF	chr1:94339740-94339890	GM12870	blood:	n/a	n/a
31	CTCF	chr1:94339723-94339916	MCF-7	breast:	n/a	n/a
32	CTCF	chr1:94339740-94339890	HCPEpiC	choroid plexus:	n/a	n/a
33	RAD21	chr1:94339598-94339996	IMR90	lung:	n/a	n/a
34	CTCF	chr1:94339715-94339936	HepG2	liver:	n/a	n/a
35	CTCF	chr1:94339760-94339910	RPTEC	kidney:	n/a	n/a
36	CTCF	chr1:94339740-94339890	GM12867	blood:	n/a	n/a
37	CTCF	chr1:94339780-94339930	GM06990	blood:	n/a	n/a
38	CTCF	chr1:94339800-94339950	HCT-116	colon:	n/a	n/a
39	CTCF	chr1:94339760-94339910	GM12871	blood:	n/a	n/a
40	CTCF	chr1:94339720-94339870	WERI-Rb-1	eye:	n/a	n/a
41	RAD21	chr1:94339667-94340060	MCF-7	breast:	n/a	n/a
42	CTCF	chr1:94339702-94339939	LNCaP	prostate:	n/a	n/a
43	CTCF	chr1:94339692-94339936	MCF-7	breast:	n/a	n/a
44	CTCF	chr1:94339762-94339876	GM20000	blood:	n/a	n/a
45	CTCF	chr1:94339655-94339889	HepG2	liver:	n/a	n/a
46	CTCF	chr1:94339740-94339890	HMF	breast:	n/a	n/a
47	POLR2A	chr1:94339537-94339890	K562	blood:	n/a	n/a
48	CTCF	chr1:94339749-94339879	GM13976	blood:	n/a	n/a
49	RAD21	chr1:94339548-94340021	MCF-7	breast:	n/a	n/a
50	RAD21	chr1:94339467-94340128	HCT-116	colon:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94336837..94340766-chr1:94341847..94346212,6	K562	blood:
2	chr1:94335249..94337846-chr1:94338670..94340764,2	K562	blood:
3	chr1:94337226..94339966-chr1:94373816..94376815,2	K562	blood:
4	chr1:94310452..94313071-chr1:94339527..94341064,2	K562	blood:
5	chr1:93811555..93814046-chr1:94339710..94342283,2	K562	blood:
6	chr1:94339429..94339939-chr1:94801277..94802005,2	MCF-7	breast:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000023909	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10489602	0.83[JPT][hapmap]
rs10489604	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs1051394	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165021	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165022	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165023	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165025	0.86[ASN][1000 genomes]
rs11165026	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029548	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029637	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029670	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140446	0.83[JPT][hapmap]
rs12758972	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1884018	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2092698	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2092699	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103784	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143992	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235971	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2273165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391315	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs2391321	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391322	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2747045	0.83[JPT][hapmap]
rs3747965	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs3789459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075523	0.83[JPT][hapmap]
rs4141737	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4240956	0.83[JPT][hapmap]
rs4847191	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4847193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847263	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4847264	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663218	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs6664719	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs6664876	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666633	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6667991	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681169	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681265	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684054	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697189	0.86[ASN][1000 genomes]
rs7364663	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs743111	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7513489	0.85[ASN][1000 genomes]
rs7513786	0.89[ASN][1000 genomes]
rs7514828	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7517632	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518940	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555136	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556047	0.82[ASN][1000 genomes]
rs7556107	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 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	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94332400-94342000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:94332800-94340800	Strong transcription	Left Ventricle	heart
6	chr1:94332800-94341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:94332800-94341600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr1:94332800-94341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:94332800-94341800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:94332800-94341800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:94332800-94341800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:94333000-94341600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:94333000-94342000	Strong transcription	Fetal Brain Female	brain
16	chr1:94333200-94341600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:94333200-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:94333400-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:94333600-94341800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:94333800-94341200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:94333800-94341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:94334000-94340800	Strong transcription	Brain Anterior Caudate	brain
25	chr1:94334000-94341200	Strong transcription	Primary T cells from cord blood	blood
26	chr1:94334000-94341200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr1:94334000-94341600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:94334000-94341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:94334000-94341600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:94334000-94341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:94334000-94341800	Strong transcription	Fetal Kidney	kidney
32	chr1:94334000-94341800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:94334000-94342000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:94334000-94343000	Strong transcription	Fetal Thymus	thymus
35	chr1:94334000-94343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:94334200-94340800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr1:94334200-94341200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:94334200-94341600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:94334200-94341600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:94334200-94341600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:94334200-94341600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:94334200-94341600	Strong transcription	Adipose Nuclei	Adipose
43	chr1:94334200-94341600	Strong transcription	Liver	Liver
44	chr1:94334200-94341600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:94334200-94341800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:94334200-94341800	Strong transcription	Brain Germinal Matrix	brain
47	chr1:94334200-94341800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr1:94334200-94342000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:94334200-94343200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr1:94334200-94343200	Strong transcription	H9 Cell Line	embryonic stem cell

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