Variant report

Variant	rs3755114
Chromosome Location	chr2:53994493-53994494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:53994390-53995707	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:53994434-53995561	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:53994442-53995493	GM12878	blood:	n/a	n/a
4	NR2F2	chr2:53994369-53995191	K562	blood:	n/a	n/a
5	HCFC1	chr2:53993642-53995965	Hela-S3	cervix:	n/a	n/a
6	RELA	chr2:53994431-53995647	GM12891	blood:	n/a	n/a
7	PML	chr2:53994367-53995329	K562	blood:	n/a	n/a
8	POLR2A	chr2:53994491-53995171	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr2:53994421-53995632	NB4	blood:	n/a	n/a
10	NFATC1	chr2:53994351-53995784	GM12878	blood:	n/a	chr2:53994386-53994399
11	POLR2A	chr2:53994421-53995461	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:53994421-53995690	Raji	blood:	n/a	n/a
13	CHD2	chr2:53994486-53995638	Hela-S3	cervix:	n/a	n/a
14	IRF1	chr2:53993929-53995175	K562	blood:	n/a	chr2:53994066-53994078 chr2:53994067-53994077 chr2:53994066-53994078 chr2:53994065-53994079
15	JUND	chr2:53994401-53995079	HepG2	liver:	n/a	chr2:53994827-53994836 chr2:53994843-53994853
16	TCF12	chr2:53994390-53995785	A549	lung:	n/a	n/a
17	SIX5	chr2:53994432-53995090	A549	lung:	n/a	chr2:53994710-53994724 chr2:53994716-53994725 chr2:53994713-53994722 chr2:53994711-53994720
18	POLR2A	chr2:53994433-53995199	HepG2	liver:	n/a	n/a
19	CTCF	chr2:53994374-53995132	K562	blood:	n/a	n/a
20	SIN3A	chr2:53994428-53995720	H1-hESC	embryonic stem cell:	n/a	chr2:53995165-53995178
21	REST	chr2:53994307-53995249	A549	lung:	n/a	n/a
22	MYC	chr2:53994263-53995599	K562	blood:	n/a	n/a
23	TAF1	chr2:53994466-53995528	GM12878	blood:	n/a	n/a
24	RCOR1	chr2:53994466-53995374	HepG2	liver:	n/a	n/a
25	POU2F2	chr2:53994479-53995360	GM12891	blood:	n/a	n/a
26	SP1	chr2:53994418-53995278	A549	lung:	n/a	n/a
27	POLR2A	chr2:53994388-53995728	GM12878	blood:	n/a	n/a
28	TAF1	chr2:53994373-53995493	A549	lung:	n/a	n/a
29	POLR2A	chr2:53994464-53994695	H1-hESC	embryonic stem cell:	n/a	n/a
30	HDAC2	chr2:53994456-53995562	MCF-7	breast:	n/a	chr2:53994827-53994841
31	POLR2A	chr2:53994291-53995350	U87	brain:	n/a	n/a
32	POLR2A	chr2:53994423-53995711	GM12891	blood:	n/a	n/a
33	TCF12	chr2:53994490-53995092	A549	lung:	n/a	n/a
34	BHLHE40	chr2:53994441-53995656	K562	blood:	n/a	n/a
35	NFIC	chr2:53994378-53995111	ECC-1	luminal epithelium:	n/a	n/a
36	MAFK	chr2:53994313-53995189	K562	blood:	n/a	chr2:53994836-53994850
37	STAT3	chr2:53994473-53995220	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:53994475-53994782	GM12878	blood:	n/a	n/a
39	BCLAF1	chr2:53994376-53995479	GM12878	blood:	n/a	chr2:53994965-53994978
40	MBD4	chr2:53994375-53995459	HepG2	liver:	n/a	n/a
41	RELA	chr2:53994483-53995560	GM19099	blood:	n/a	n/a
42	POLR2A	chr2:53994323-53995521	K562	blood:	n/a	n/a
43	TEAD4	chr2:53994462-53995367	K562	blood:	n/a	n/a
44	YY1	chr2:53994457-53995611	GM12878	blood:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
45	SIX5	chr2:53994492-53994992	K562	blood:	n/a	chr2:53994710-53994724 chr2:53994716-53994725 chr2:53994713-53994722 chr2:53994711-53994720
46	ZEB1	chr2:53994492-53994803	GM12878	blood:	n/a	n/a
47	NFIC	chr2:53994329-53995064	HepG2	liver:	n/a	n/a
48	GABPA	chr2:53994434-53995020	A549	lung:	n/a	chr2:53994912-53994926 chr2:53994915-53994926 chr2:53994915-53994929
49	POLR2A	chr2:53994411-53995668	HepG2	liver:	n/a	n/a
50	BCL3	chr2:53994333-53995803	A549	lung:	n/a	chr2:53994965-53994978

No.	Distal block	Cell Line	Cell type
1	chr2:53780507..53782864-chr2:53992929..53994536,2	K562	blood:
2	chr2:53994288..53995047-chr2:105953823..105954384,2	HCT-116	colon:
3	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
4	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
5	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
CHAC2	TF binding region
GPR75-ASB3	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction
ENSG00000272994	Chromatin interaction
ENSG00000135974	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10204047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10204432	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10490472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13387421	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13404007	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13426962	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17039534	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17045069	0.83[AMR][1000 genomes]
rs17045109	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045296	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056650	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2287339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2287347	0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[ASN][1000 genomes]
rs2302876	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28834518	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3213768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213774	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755116	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];0.99[ASN][1000 genomes]
rs3755119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770391	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];0.99[ASN][1000 genomes]
rs3770396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3815650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821079	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59951261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60972886	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545368	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6724214	0.88[ASN][1000 genomes]
rs6761242	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72799242	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72799275	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72901302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72902916	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72902923	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72902926	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72902929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7601553	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs997643	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr2:53986400-53994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:53990800-53994600	Weak transcription	Gastric	stomach
3	chr2:53990800-53994600	Weak transcription	Pancreas	Pancrea
4	chr2:53990800-53994600	Weak transcription	Spleen	Spleen
5	chr2:53990800-53994800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:53994000-53994800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:53994000-53995200	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr2:53994000-53995200	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:53994000-53995800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:53994000-53996200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:53994200-53994600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:53994200-53994600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:53994200-53994600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr2:53994200-53994600	Flanking Active TSS	Liver	Liver
15	chr2:53994200-53994600	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr2:53994200-53994600	Weak transcription	Small Intestine	intestine
17	chr2:53994200-53994600	Flanking Active TSS	Thymus	Thymus
18	chr2:53994200-53994600	Flanking Active TSS	NHEK	skin
19	chr2:53994200-53994800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr2:53994200-53994800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:53994200-53994800	Flanking Active TSS	HUVEC	blood vessel
22	chr2:53994200-53995000	Active TSS	Brain Germinal Matrix	brain
23	chr2:53994200-53995000	Active TSS	Right Atrium	heart
24	chr2:53994200-53995400	Active TSS	Fetal Muscle Trunk	muscle
25	chr2:53994200-53995400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:53994200-53995600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:53994200-53995600	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:53994200-53995600	Active TSS	HSMMtube	muscle
29	chr2:53994200-53995600	Active TSS	NHLF	lung
30	chr2:53994200-53995800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:53994200-53995800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:53994200-53995800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:53994200-53995800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:53994200-53995800	Active TSS	Psoas Muscle	Psoas
35	chr2:53994200-53995800	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr2:53994200-53995800	Active TSS	HMEC	breast
37	chr2:53994200-53996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:53994200-53996000	Active TSS	GM12878-XiMat	blood
39	chr2:53994200-53996000	Active TSS	K562	blood
40	chr2:53994200-53996200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr2:53994200-53996400	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:53994200-53996400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr2:53994400-53994600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:53994400-53994600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr2:53994400-53994600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr2:53994400-53994600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:53994400-53994600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:53994400-53994600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:53994400-53994600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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