Variant report

Variant	rs3812062
Chromosome Location	chr5:126112283-126112284
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	CEBPB	chr5:126111696-126112501	GM12878	blood:	n/a	chr5:126112256-126112273
2	MAX	chr5:126112044-126114710	HCT-116	colon:	n/a	n/a
3	POLR2A	chr5:126111728-126114531	PFSK-1	brain:	n/a	n/a
4	GATA3	chr5:126111973-126113276	A549	lung:	n/a	n/a
5	POLR2A	chr5:126111057-126115293	GM12878	blood:	n/a	n/a
6	ATF3	chr5:126112091-126112641	K562	blood:	n/a	n/a
7	ZEB1	chr5:126112245-126112711	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:126112099-126114877	GM12878	blood:	n/a	n/a
9	ELF1	chr5:126112011-126112883	MCF-7	breast:	n/a	n/a
10	RELA	chr5:126111991-126114834	GM15510	blood:	n/a	n/a
11	ZEB1	chr5:126112143-126112442	GM12878	blood:	n/a	n/a
12	TAF1	chr5:126112166-126112424	PFSK-1	brain:	n/a	n/a
13	MAX	chr5:126111958-126115083	NB4	blood:	n/a	chr5:126114904-126114913 chr5:126114903-126114913 chr5:126114903-126114914 chr5:126114905-126114912 chr5:126114902-126114915
14	ZNF143	chr5:126112175-126113012	K562	blood:	n/a	n/a
15	CEBPD	chr5:126112039-126113599	K562	blood:	n/a	n/a
16	POLR2A	chr5:126111237-126115281	GM12891	blood:	n/a	n/a
17	WRNIP1	chr5:126112175-126112489	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:126112037-126112758	GM12891	blood:	n/a	n/a
19	ELK4	chr5:126112207-126112595	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:126112012-126114517	HUVEC	blood vessel:	n/a	n/a
21	USF1	chr5:126112194-126113177	K562	blood:	n/a	n/a
22	E2F4	chr5:126112118-126114460	Hela-S3	cervix:	n/a	chr5:126114123-126114133 chr5:126114123-126114134 chr5:126114124-126114131 chr5:126112178-126112193 chr5:126114123-126114131 chr5:126114124-126114132 chr5:126114124-126114135 chr5:126113879-126113888 chr5:126114124-126114132
23	NFIC	chr5:126111055-126113198	GM12878	blood:	n/a	n/a
24	MAZ	chr5:126111857-126114511	IMR90	lung:	n/a	n/a
25	POLR2A	chr5:126111998-126114762	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:126111543-126115014	Hela-S3	cervix:	n/a	n/a
27	ATF3	chr5:126112142-126112730	A549	lung:	n/a	n/a
28	CREB1	chr5:126112276-126112795	ECC-1	luminal epithelium:	n/a	n/a
29	RELA	chr5:126111954-126113061	GM19099	blood:	n/a	n/a
30	ATF2	chr5:126111922-126113195	GM12878	blood:	n/a	chr5:126112262-126112269
31	POLR2A	chr5:126112075-126114546	H1-neurons	neurons:	n/a	n/a
32	FOXA2	chr5:126112280-126112743	A549	lung:	n/a	n/a
33	RFX5	chr5:126112032-126114607	Hela-S3	cervix:	n/a	n/a
34	MYC	chr5:126112034-126113222	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr5:126112079-126114876	Hela-S3	cervix:	n/a	n/a
36	SP1	chr5:126112111-126112805	HepG2	liver:	n/a	chr5:126112791-126112802 chr5:126112766-126112777
37	TAF1	chr5:126112201-126114448	H1-neurons	neurons:	n/a	n/a
38	STAT3	chr5:126111952-126112442	GM12878	blood:	n/a	chr5:126112400-126112411
39	GABPA	chr5:126112150-126112889	MCF-7	breast:	n/a	n/a
40	CTCF	chr5:126112240-126112390	HMEC	breast:	n/a	n/a
41	IRF1	chr5:126112225-126113031	K562	blood:	n/a	n/a
42	REST	chr5:126112182-126112712	HepG2	liver:	n/a	chr5:126112274-126112281
43	ATF1	chr5:126112091-126112779	K562	blood:	n/a	n/a
44	HDAC2	chr5:126111996-126112683	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:126111809-126115016	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr5:126112100-126114978	K562	blood:	n/a	chr5:126114904-126114913 chr5:126114903-126114913 chr5:126114903-126114914 chr5:126114905-126114912 chr5:126114902-126114915
47	MYC	chr5:126112215-126113008	K562	blood:	n/a	n/a
48	NFYB	chr5:126111791-126112859	GM12878	blood:	n/a	chr5:126112686-126112701
49	CEBPB	chr5:126112004-126112731	MCF-7	breast:	n/a	chr5:126112256-126112273
50	MTA3	chr5:126111595-126113716	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1713063..1714611-chr5:126112187..126114301,2	MCF-7	breast:
2	chr5:126089250..126100296-chr5:126109758..126119075,20	K562	blood:
3	chr11:11863562..11864491-chr5:126112074..126112673,2	Hela-S3	cervix:

Variant related genes	Relation type
LMNB1	TF binding region
ENSG00000251072	TF binding region
ENSG00000252185	Chromatin interaction
ENSG00000270195	Chromatin interaction
ENSG00000170242	Chromatin interaction
ENSG00000163950	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12514703	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12514978	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12515255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12515582	1.00[CEU][hapmap]
rs12517303	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12518228	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12518331	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520218	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12521266	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17165305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17165351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17165359	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2230151	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34364708	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3749830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805737	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55699774	0.92[ASN][1000 genomes]
rs55924928	0.84[AMR][1000 genomes]
rs56052550	0.84[AMR][1000 genomes]
rs56121757	1.00[ASN][1000 genomes]
rs56366269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58103919	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58418743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59395878	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60107783	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60147760	1.00[ASN][1000 genomes]
rs60818126	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61074663	0.92[ASN][1000 genomes]
rs61383192	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780203	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72780207	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72780210	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72780211	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72780212	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780215	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780216	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780217	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780218	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780220	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72780222	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72798238	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72798243	1.00[ASN][1000 genomes]
rs72798245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798246	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72798247	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72798249	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72798253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72798255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7447810	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126111200-126112400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr5:126111200-126112400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:126111200-126112400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr5:126111200-126112600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:126111200-126112800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:126111200-126113400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:126111200-126113400	Active TSS	Fetal Brain Female	brain
8	chr5:126111200-126114400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:126111200-126114600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:126111200-126114600	Active TSS	NHLF	lung
11	chr5:126111200-126115000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:126111200-126115400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:126111200-126115800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:126111200-126115800	Active TSS	A549	lung
15	chr5:126111400-126112400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr5:126111400-126113000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:126111400-126113600	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:126111400-126114200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:126111400-126114400	Active TSS	Fetal Intestine Small	intestine
20	chr5:126111400-126114600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:126111400-126114800	Active TSS	NHDF-Ad	bronchial
22	chr5:126111400-126115000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:126111400-126115200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr5:126111400-126115200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr5:126111600-126112400	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr5:126111600-126112400	Flanking Active TSS	NHEK	skin
27	chr5:126111600-126112600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr5:126111600-126113000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:126111600-126113000	Active TSS	HepG2	liver
30	chr5:126111600-126113200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:126111600-126113200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr5:126111600-126113400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:126111600-126113800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:126111600-126114200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr5:126111600-126114400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:126111600-126114400	Active TSS	Fetal Lung	lung
37	chr5:126111600-126114400	Active TSS	HMEC	breast
38	chr5:126111600-126114400	Active TSS	HSMM	muscle
39	chr5:126111600-126114400	Active TSS	K562	blood
40	chr5:126111600-126114600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:126111600-126114600	Active TSS	Fetal Intestine Large	intestine
42	chr5:126111600-126114800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr5:126111600-126115000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr5:126111600-126116000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:126111600-126116000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:126111600-126116200	Active TSS	Thymus	Thymus
47	chr5:126111600-126116600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr5:126111800-126112400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr5:126111800-126112400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr5:126111800-126112400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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