Variant report

Variant	rs2287342
Chromosome Location	chr2:54014558-54014559
allele	G/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	chr2:54013517-54014999	Hela-S3	cervix:	n/a	n/a
2	SIN3AK20	chr2:54013700-54014760	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr2:54013277-54015089	H1-neurons	neurons:	n/a	n/a
4	CBX3	chr2:54013545-54014566	K562	blood:	n/a	n/a
5	POLR2A	chr2:54013384-54015113	Hela-S3	cervix:	n/a	n/a
6	ZNF263	chr2:54013593-54015150	HEK293-T-REx	kidney:	n/a	chr2:54014264-54014285
7	SIN3AK20	chr2:54013582-54014685	K562	blood:	n/a	n/a
8	MAX	chr2:54013442-54015420	Hela-S3	cervix:	n/a	n/a
9	CREB1	chr2:54013695-54014565	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr2:54013774-54014599	PANC-1	pancreas:	n/a	n/a
11	GABPA	chr2:54013450-54014856	A549	lung:	n/a	chr2:54014079-54014088
12	POLR2A	chr2:54013408-54014594	K562	blood:	n/a	n/a
13	MXI1	chr2:54013208-54015472	IMR90	lung:	n/a	n/a
14	POLR2A	chr2:54013427-54014597	GM18505	blood:	n/a	n/a
15	POLR2A	chr2:54013413-54014891	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr2:54013422-54014636	K562	blood:	n/a	n/a
17	RAD21	chr2:54014338-54014572	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr2:54012927-54015605	IMR90	lung:	n/a	chr2:54013359-54013367
19	POLR2A	chr2:54013705-54014692	Gliobla	brain:	n/a	n/a
20	MXI1	chr2:54013439-54015410	HepG2	liver:	n/a	n/a
21	MAZ	chr2:54013489-54014841	K562	blood:	n/a	n/a
22	TCF12	chr2:54013367-54014955	A549	lung:	n/a	n/a
23	POLR2A	chr2:54013342-54014661	GM12892	blood:	n/a	n/a
24	POLR2A	chr2:54013509-54014759	K562	blood:	n/a	n/a
25	GABPA	chr2:54013618-54014621	HL-60	blood:	n/a	chr2:54014079-54014088
26	GTF2F1	chr2:54013445-54015193	Hela-S3	cervix:	n/a	n/a
27	BCL3	chr2:54013707-54014880	A549	lung:	n/a	chr2:54014527-54014540 chr2:54013932-54013945
28	TBL1XR1	chr2:54013959-54014608	K562	blood:	n/a	n/a
29	RELA	chr2:54013632-54014637	GM15510	blood:	n/a	n/a
30	HEY1	chr2:54013495-54014565	HepG2	liver:	n/a	n/a
31	GABPA	chr2:54013788-54014637	K562	blood:	n/a	chr2:54014079-54014088
32	POLR2A	chr2:54013442-54015119	HL-60	blood:	n/a	n/a
33	POLR2A	chr2:54013694-54014565	PANC-1	pancreas:	n/a	n/a
34	YY1	chr2:54013388-54014572	GM12878	blood:	n/a	chr2:54013780-54013790 chr2:54013564-54013572
35	SIN3A	chr2:54013378-54014918	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:54013302-54014592	GM12892	blood:	n/a	n/a
37	POLR2A	chr2:54013414-54014705	GM12891	blood:	n/a	n/a
38	POLR2A	chr2:54013432-54014558	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:54013420-54014657	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:54013513-54014619	U87	brain:	n/a	n/a
41	MAX	chr2:54013451-54014565	MCF-7	breast:	n/a	n/a
42	POLR2A	chr2:54013852-54014614	HUVEC	blood vessel:	n/a	n/a
43	MAX	chr2:54013702-54014605	SK-N-SH	brain:	n/a	n/a
44	TAF1	chr2:54013508-54014741	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr2:54013158-54015202	PBDE	blood:	n/a	n/a
46	CREB1	chr2:54013279-54015014	HepG2	liver:	n/a	n/a
47	CTCF	chr2:54014114-54014587	K562	blood:	n/a	n/a
48	POLR2A	chr2:54013542-54014559	HEK293	kidney:	n/a	n/a
49	SIN3A	chr2:54013182-54015158	H1-hESC	embryonic stem cell:	n/a	n/a
50	HEY1	chr2:54013415-54014744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54014148..54016031-chr2:54196984..54199909,2	MCF-7	breast:
2	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
3	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:
4	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000115239	Chromatin interaction
ENSG00000143942	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10204047	0.92[EUR][1000 genomes]
rs10204432	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10490472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs13387421	0.97[EUR][1000 genomes]
rs13404007	0.97[EUR][1000 genomes]
rs13426962	1.00[EUR][1000 genomes]
rs17039534	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045109	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045123	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045296	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2056650	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2287339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287347	0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.84[ASN][1000 genomes]
rs2302876	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28834518	0.95[EUR][1000 genomes];0.82[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];0.93[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3213774	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs3755114	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]
rs3755115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815650	0.93[EUR][1000 genomes]
rs3821079	0.97[EUR][1000 genomes]
rs59951261	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60972886	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545368	0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6724214	0.86[ASN][1000 genomes]
rs6761242	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72799242	0.97[EUR][1000 genomes]
rs72799275	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72901302	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72902916	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72902923	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72902926	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72902929	0.97[EUR][1000 genomes]
rs7601553	0.86[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][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	chr2:54011800-54015800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:54012200-54014800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:54012200-54015000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:54012200-54015800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:54012200-54015800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54012400-54014800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:54012400-54015400	Active TSS	Hela-S3	cervix
8	chr2:54012400-54015600	Active TSS	GM12878-XiMat	blood
9	chr2:54012400-54015800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:54012400-54015800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:54012400-54015800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:54012400-54016000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:54012600-54015200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:54012600-54015200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:54012600-54015400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:54012600-54015400	Active TSS	Fetal Kidney	kidney
17	chr2:54012600-54015400	Active TSS	NHDF-Ad	bronchial
18	chr2:54012600-54015600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr2:54012600-54015600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:54012600-54015600	Active TSS	Colonic Mucosa	Colon
21	chr2:54012600-54015600	Active TSS	K562	blood
22	chr2:54012600-54015800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:54012600-54015800	Active TSS	NHLF	lung
24	chr2:54012800-54014600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:54012800-54014800	Active TSS	Brain Angular Gyrus	brain
26	chr2:54012800-54015000	Active TSS	Brain Substantia Nigra	brain
27	chr2:54012800-54015000	Active TSS	Colon Smooth Muscle	Colon
28	chr2:54012800-54015200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:54012800-54015200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:54012800-54015200	Active TSS	Ovary	ovary
31	chr2:54012800-54015400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:54012800-54015400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:54012800-54015400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:54012800-54015600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:54013000-54014600	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr2:54013000-54014600	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:54013000-54014800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:54013000-54014800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:54013000-54014800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr2:54013000-54014800	Active TSS	Fetal Heart	heart
41	chr2:54013000-54014800	Active TSS	Fetal Lung	lung
42	chr2:54013000-54014800	Active TSS	Fetal Thymus	thymus
43	chr2:54013000-54015000	Active TSS	Fetal Brain Male	brain
44	chr2:54013000-54015000	Active TSS	Fetal Stomach	stomach
45	chr2:54013000-54015000	Active TSS	Stomach Smooth Muscle	stomach
46	chr2:54013000-54015000	Active TSS	Dnd41	blood
47	chr2:54013000-54015200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:54013000-54015200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:54013000-54015200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:54013000-54015200	Active TSS	Left Ventricle	heart

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