Variant report

Variant	rs17045203
Chromosome Location	chr2:53994820-53994821
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	ZNF263	chr2:53994532-53995418	HEK293-T-REx	kidney:	n/a	n/a
2	CTCF	chr2:53994800-53994950	HVMF	connective:	n/a	n/a
3	POLR2A	chr2:53994390-53995707	SK-N-MC	brain:	n/a	n/a
4	PAX5	chr2:53994700-53995266	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:53994434-53995561	GM12878	blood:	n/a	n/a
6	GATA2	chr2:53994546-53995474	SH-SY5Y	brain:	n/a	chr2:53994842-53994849
7	POLR2A	chr2:53994442-53995493	GM12878	blood:	n/a	n/a
8	NR2F2	chr2:53994369-53995191	K562	blood:	n/a	n/a
9	HCFC1	chr2:53993642-53995965	Hela-S3	cervix:	n/a	n/a
10	RELA	chr2:53994495-53995564	GM19193	blood:	n/a	n/a
11	RELA	chr2:53994431-53995647	GM12891	blood:	n/a	n/a
12	CTCF	chr2:53994720-53994870	HFF	foreskin:	n/a	n/a
13	PML	chr2:53994367-53995329	K562	blood:	n/a	n/a
14	YY1	chr2:53994509-53995639	SK-N-SH	brain:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
15	NR2F2	chr2:53994512-53995387	K562	blood:	n/a	n/a
16	POLR2A	chr2:53994491-53995171	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr2:53994421-53995632	NB4	blood:	n/a	n/a
18	NFATC1	chr2:53994351-53995784	GM12878	blood:	n/a	chr2:53994386-53994399
19	CTCF	chr2:53994790-53995086	K562	blood:	n/a	n/a
20	POLR2A	chr2:53994421-53995461	GM12878	blood:	n/a	n/a
21	YY1	chr2:53994788-53995202	K562	blood:	n/a	chr2:53994965-53994979 chr2:53994922-53994936 chr2:53994918-53994932 chr2:53994968-53994977
22	CTCF	chr2:53994820-53994970	HPAF	blood vessel:	n/a	n/a
23	POLR2A	chr2:53994421-53995690	Raji	blood:	n/a	n/a
24	CTBP2	chr2:53994706-53995554	H1-hESC	embryonic stem cell:	n/a	n/a
25	CHD2	chr2:53994486-53995638	Hela-S3	cervix:	n/a	n/a
26	MAFF	chr2:53994636-53994995	HepG2	liver:	n/a	n/a
27	BRCA1	chr2:53994541-53995217	HepG2	liver:	n/a	n/a
28	IRF1	chr2:53993929-53995175	K562	blood:	n/a	chr2:53994066-53994078 chr2:53994067-53994077 chr2:53994066-53994078 chr2:53994065-53994079
29	TAF1	chr2:53994807-53995527	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr2:53994401-53995079	HepG2	liver:	n/a	chr2:53994827-53994836 chr2:53994843-53994853
31	TAF1	chr2:53994805-53995105	PFSK-1	brain:	n/a	n/a
32	TCF12	chr2:53994390-53995785	A549	lung:	n/a	n/a
33	SIX5	chr2:53994432-53995090	A549	lung:	n/a	chr2:53994710-53994724 chr2:53994716-53994725 chr2:53994713-53994722 chr2:53994711-53994720
34	GTF2F1	chr2:53994796-53995086	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:53994433-53995199	HepG2	liver:	n/a	n/a
36	TBL1XR1	chr2:53994525-53995396	K562	blood:	n/a	n/a
37	CTCF	chr2:53994374-53995132	K562	blood:	n/a	n/a
38	SIN3A	chr2:53994428-53995720	H1-hESC	embryonic stem cell:	n/a	chr2:53995165-53995178
39	REST	chr2:53994307-53995249	A549	lung:	n/a	n/a
40	MYC	chr2:53994263-53995599	K562	blood:	n/a	n/a
41	TAF1	chr2:53994466-53995528	GM12878	blood:	n/a	n/a
42	RCOR1	chr2:53994466-53995374	HepG2	liver:	n/a	n/a
43	POU2F2	chr2:53994479-53995360	GM12891	blood:	n/a	n/a
44	SP1	chr2:53994418-53995278	A549	lung:	n/a	n/a
45	RCOR1	chr2:53994529-53995051	K562	blood:	n/a	n/a
46	POLR2A	chr2:53994388-53995728	GM12878	blood:	n/a	n/a
47	TAF1	chr2:53994373-53995493	A549	lung:	n/a	n/a
48	CTCF	chr2:53994798-53995103	H1-hESC	embryonic stem cell:	n/a	n/a
49	HDAC2	chr2:53994456-53995562	MCF-7	breast:	n/a	chr2:53994827-53994841
50	POLR2A	chr2:53994291-53995350	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:53994500..53995088-chr5:176784213..176785083,2	NB4	blood:
2	chr12:120730450..120731263-chr2:53994688..53995293,2	Hela-S3	cervix:
3	chr2:53994288..53995047-chr2:105953823..105954384,2	HCT-116	colon:
4	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
5	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
6	chr1:151512354..151513189-chr2:53994612..53995352,2	Hela-S3	cervix:
7	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
CHAC2	TF binding region
GPR75-ASB3	TF binding region
ENSG00000272994	Chromatin interaction
ENSG00000169220	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000115239	Chromatin interaction
ENSG00000135974	Chromatin interaction
ENSG00000068912	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs11897282	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11901698	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs1232	0.84[CHB][hapmap]
rs13408029	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17045176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17520505	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17520854	0.85[AMR][1000 genomes]
rs17521008	0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2287340	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302797	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2542572	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2542573	0.82[ASN][1000 genomes]
rs2542578	0.80[ASN][1000 genomes]
rs2542580	0.81[ASN][1000 genomes]
rs2542581	0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs2542582	0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2542583	0.91[ASN][1000 genomes]
rs2542589	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2542590	0.83[ASN][1000 genomes]
rs2542591	0.92[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs2542592	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs2543629	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2692519	0.92[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs2692522	0.82[ASN][1000 genomes]
rs2692523	0.80[ASN][1000 genomes]
rs2692530	0.89[ASN][1000 genomes]
rs2692533	0.92[CHB][hapmap];0.96[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2692535	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2909262	0.90[ASN][1000 genomes]
rs2949813	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35772199	0.83[ASN][1000 genomes]
rs3770394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770395	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770397	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770399	0.85[ASN][1000 genomes]
rs3770411	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs3922262	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4116709	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs55897904	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58326257	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137573	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137602	0.83[ASN][1000 genomes]
rs62137606	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137610	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137611	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137612	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730006	0.88[ASN][1000 genomes]
rs719127	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs72901256	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7600817	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805316	0.84[CHB][hapmap]
rs805334	0.81[CHB][hapmap]
rs805338	0.84[CHB][hapmap]
rs805435	0.81[ASN][1000 genomes]
rs805437	0.84[CHB][hapmap]
rs805446	0.84[CHB][hapmap]
rs805447	0.84[CHB][hapmap]
rs805449	0.82[CHB][hapmap]

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	chr2:53994000-53995200	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr2:53994000-53995200	Active TSS	Stomach Smooth Muscle	stomach
3	chr2:53994000-53995800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:53994000-53996200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:53994200-53995000	Active TSS	Brain Germinal Matrix	brain
6	chr2:53994200-53995000	Active TSS	Right Atrium	heart
7	chr2:53994200-53995400	Active TSS	Fetal Muscle Trunk	muscle
8	chr2:53994200-53995400	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr2:53994200-53995600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:53994200-53995600	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:53994200-53995600	Active TSS	HSMMtube	muscle
12	chr2:53994200-53995600	Active TSS	NHLF	lung
13	chr2:53994200-53995800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:53994200-53995800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr2:53994200-53995800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:53994200-53995800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:53994200-53995800	Active TSS	Psoas Muscle	Psoas
18	chr2:53994200-53995800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr2:53994200-53995800	Active TSS	HMEC	breast
20	chr2:53994200-53996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:53994200-53996000	Active TSS	GM12878-XiMat	blood
22	chr2:53994200-53996000	Active TSS	K562	blood
23	chr2:53994200-53996200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:53994200-53996400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:53994200-53996400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:53994400-53995200	Active TSS	Primary hematopoietic stem cells	blood
28	chr2:53994400-53995200	Active TSS	Adipose Nuclei	Adipose
29	chr2:53994400-53995200	Active TSS	Fetal Muscle Leg	muscle
30	chr2:53994400-53995400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:53994400-53995400	Active TSS	Primary B cells from peripheral blood	blood
32	chr2:53994400-53995400	Active TSS	Primary T cells from cord blood	blood
33	chr2:53994400-53995400	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:53994400-53995400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:53994400-53995400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:53994400-53995400	Active TSS	Brain Hippocampus Middle	brain
37	chr2:53994400-53995400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr2:53994400-53995400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:53994400-53995400	Active TSS	Brain Substantia Nigra	brain
40	chr2:53994400-53995400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:53994400-53995400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:53994400-53995400	Active TSS	Fetal Brain Male	brain
43	chr2:53994400-53995400	Active TSS	Fetal Heart	heart
44	chr2:53994400-53995400	Active TSS	Fetal Lung	lung
45	chr2:53994400-53995400	Active TSS	Lung	lung
46	chr2:53994400-53995400	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr2:53994400-53995400	Bivalent/Poised TSS	HepG2	liver
48	chr2:53994400-53995600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:53994400-53995600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:53994400-53995600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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