Variant report

Variant	rs13425086
Chromosome Location	chr2:38893184-38893185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:280)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:280 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:38892829-38894057	K562	blood:	n/a	n/a
2	FOXA1	chr2:38893049-38893383	T-47D	breast:	n/a	n/a
3	EP300	chr2:38892809-38893303	SK-N-SH_RA	brain:	n/a	chr2:38893161-38893174
4	POLR2A	chr2:38892931-38893480	ECC-1	luminal epithelium:	n/a	n/a
5	FOXA2	chr2:38892905-38893561	A549	lung:	n/a	n/a
6	POLR2A	chr2:38893118-38893461	U87	brain:	n/a	n/a
7	RCOR1	chr2:38892809-38893876	HepG2	liver:	n/a	n/a
8	SP1	chr2:38892751-38893877	A549	lung:	n/a	chr2:38893855-38893865 chr2:38893855-38893865
9	USF1	chr2:38892901-38893271	A549	lung:	n/a	n/a
10	SIX5	chr2:38892750-38893259	GM12878	blood:	n/a	chr2:38893020-38893034
11	ETS1	chr2:38892704-38893907	A549	lung:	n/a	chr2:38892985-38892998 chr2:38893021-38893034
12	EP300	chr2:38892858-38893211	H1-hESC	embryonic stem cell:	n/a	chr2:38893161-38893174
13	SIX5	chr2:38892644-38893580	A549	lung:	n/a	chr2:38893020-38893034
14	YY1	chr2:38892852-38893350	ECC-1	luminal epithelium:	n/a	n/a
15	TFAP2A	chr2:38892806-38893676	Hela-S3	cervix:	n/a	chr2:38893105-38893116 chr2:38893104-38893118 chr2:38893106-38893116 chr2:38893134-38893146 chr2:38893106-38893116 chr2:38893130-38893145 chr2:38893134-38893146 chr2:38893104-38893119 chr2:38893523-38893535 chr2:38893134-38893146 chr2:38893104-38893118 chr2:38893106-38893116
16	POLR2A	chr2:38893020-38893433	U87	brain:	n/a	n/a
17	ZNF143	chr2:38892751-38893433	K562	blood:	n/a	chr2:38892986-38893004 chr2:38893022-38893040 chr2:38893029-38893044
18	HEY1	chr2:38893108-38893527	K562	blood:	n/a	n/a
19	RAD21	chr2:38892810-38893431	SK-N-SH_RA	brain:	n/a	n/a
20	KAP1	chr2:38892852-38893642	HEK293	kidney:	n/a	n/a
21	POLR2A	chr2:38892828-38893837	HepG2	liver:	n/a	n/a
22	SIN3AK20	chr2:38892856-38893525	SK-N-SH	brain:	n/a	n/a
23	TAF1	chr2:38893097-38893476	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:38892952-38893488	HUVEC	blood vessel:	n/a	n/a
25	SIN3AK20	chr2:38892961-38893415	PFSK-1	brain:	n/a	n/a
26	TAF1	chr2:38893130-38893439	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr2:38893140-38893290	HPAF	blood vessel:	n/a	n/a
28	GTF2F1	chr2:38892940-38893297	H1-hESC	embryonic stem cell:	n/a	n/a
29	HEY1	chr2:38892815-38893998	HepG2	liver:	n/a	n/a
30	MAFK	chr2:38892943-38893343	HepG2	liver:	n/a	n/a
31	EP300	chr2:38892782-38893487	HepG2	liver:	n/a	chr2:38893161-38893174
32	SP1	chr2:38892722-38893969	HepG2	liver:	n/a	chr2:38893855-38893865 chr2:38893855-38893865
33	ATF3	chr2:38892941-38893712	A549	lung:	n/a	n/a
34	CEBPB	chr2:38892878-38893189	K562	blood:	n/a	n/a
35	ELF1	chr2:38892795-38893417	HepG2	liver:	n/a	n/a
36	ZNF384	chr2:38892422-38893394	K562	blood:	n/a	n/a
37	RCOR1	chr2:38892896-38894155	K562	blood:	n/a	n/a
38	CHD2	chr2:38892870-38893193	K562	blood:	n/a	n/a
39	RCOR1	chr2:38892900-38893687	Hela-S3	cervix:	n/a	n/a
40	E2F6	chr2:38893004-38893798	A549	lung:	n/a	n/a
41	BRCA1	chr2:38892854-38893467	Hela-S3	cervix:	n/a	n/a
42	MAX	chr2:38892878-38893808	Hela-S3	cervix:	n/a	n/a
43	SIX5	chr2:38892782-38893245	K562	blood:	n/a	chr2:38893020-38893034
44	CCNT2	chr2:38892868-38893878	K562	blood:	n/a	n/a
45	POLR2A	chr2:38893065-38893468	HCT-116	colon:	n/a	n/a
46	MAX	chr2:38892738-38894042	A549	lung:	n/a	n/a
47	POLR2A	chr2:38892833-38893492	HCT-116	colon:	n/a	n/a
48	POLR2A	chr2:38892715-38893554	PFSK-1	brain:	n/a	n/a
49	TEAD4	chr2:38892814-38893261	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:38893058-38893466	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:38893161-38893211	NHDF-neo	bronchial:	n/a
2	chr2:38893161-38893211	AG09319	gingival:	n/a
3	chr2:38893161-38893211	MCF10A-Er-Src	breast:	n/a
4	chr2:38893161-38893211	SK-N-MC	brain:	n/a
5	chr2:38893161-38893211	SAEC	small airway:	n/a
6	chr2:38893161-38893211	HIPEpiC	eye:	n/a
7	chr2:38893161-38893211	ovcar-3	ovarian:	n/a
8	chr2:38893161-38893211	K562	blood:	n/a
9	chr2:38893161-38893211	HRE	kidney:	n/a
10	chr2:38893161-38893211	U87	brain:	n/a
11	chr2:38893161-38893211	GM12878	blood:	n/a
12	chr2:38893161-38893211	T-47D	breast:	n/a
13	chr2:38893161-38893211	PrEC	prostate:	n/a
14	chr2:38893161-38893211	HEK293	kidney:	embryo
15	chr2:38893161-38893211	HRCEpiC	kidney:	n/a
16	chr2:38893161-38893211	GM12891	blood:	n/a
17	chr2:38893161-38893211	SKMC	muscle:	n/a
18	chr2:38893161-38893211	PFSK-1	brain:	n/a
19	chr2:38893161-38893211	Caco-2	colon:	n/a
20	chr2:38893161-38893211	HUVEC	blood vessel:	n/a
21	chr2:38893161-38893211	Hela-S3	cervix:	n/a
22	chr2:38893161-38893211	ProgFib	skin:	n/a
23	chr2:38893161-38893211	AG10803	skin:	n/a
24	chr2:38893161-38893211	AG04449	skin:	fetal
25	chr2:38893161-38893211	SK-N-SH_RA	brain:	n/a
26	chr2:38893161-38893211	Hepatocyte	liver:	n/a
27	chr2:38893161-38893211	HMEC	breast:	n/a
28	chr2:38893161-38893211	CMK	blood:	n/a
29	chr2:38893161-38893211	RPTEC	kidney:	n/a
30	chr2:38893161-38893211	HCPEpiC	choroid plexus:	n/a
31	chr2:38893161-38893211	HAEpiC	amniotic membrane:	n/a
32	chr2:38893161-38893211	Jurkat	blood:	n/a
33	chr2:38893161-38893211	PANC-1	pancreas:	n/a
34	chr2:38893161-38893211	HPAEpiC	pulmonary alveolar:	n/a
35	chr2:38893161-38893211	AG09309	skin:	n/a
36	chr2:38893161-38893211	HCM	heart:	n/a
37	chr2:38893161-38893211	GM12892	blood:	n/a
38	chr2:38893161-38893211	HRPEpiC	eye:	n/a
39	chr2:38893161-38893211	MCF-7	breast:	n/a
40	chr2:38893161-38893211	HCF	heart:	n/a
41	chr2:38893161-38893211	A549	lung:	n/a
42	chr2:38893161-38893211	NHBE	bronchial:	n/a
43	chr2:38893161-38893211	AoSMC	blood vessel:	n/a
44	chr2:38893161-38893211	BJ	skin:	n/a
45	chr2:38893161-38893211	GM19239	blood:	n/a
46	chr2:38893161-38893211	HEEpiC	esophagus:	n/a
47	chr2:38893161-38893211	NH-A	brain:	n/a
48	chr2:38893161-38893211	HCT-116	colon:	n/a
49	chr2:38893161-38893211	NB4	blood:	n/a
50	chr2:38893161-38893211	HepG2	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:38892007..38895113-chr2:38976994..38979857,4	K562	blood:
2	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
3	chr2:38891821..38893324-chr2:38896247..38899182,2	K562	blood:
4	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
5	chr2:38829496..38831232-chr2:38893143..38894875,2	MCF-7	breast:
6	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:

No data

Variant related genes	Relation type
GALM	TF binding region
GALM	CpG island
ENSG00000232518	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11688977	0.94[EUR][1000 genomes]
rs11689051	0.88[EUR][1000 genomes]
rs12478924	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712609	0.95[EUR][1000 genomes]
rs12712612	0.91[ASN][1000 genomes]
rs13004674	0.82[ASN][1000 genomes]
rs13004806	0.82[ASN][1000 genomes]
rs13004842	0.82[ASN][1000 genomes]
rs13005073	0.82[ASN][1000 genomes]
rs13011383	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13016907	0.89[ASN][1000 genomes]
rs13029674	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032255	0.92[ASN][1000 genomes]
rs13383762	0.89[ASN][1000 genomes]
rs13387464	0.95[EUR][1000 genomes]
rs17576472	0.91[ASN][1000 genomes]
rs17576507	0.89[ASN][1000 genomes]
rs2373424	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28716236	0.93[ASN][1000 genomes]
rs34391548	0.91[ASN][1000 genomes]
rs34533539	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34756536	0.89[ASN][1000 genomes]
rs34875979	0.87[ASN][1000 genomes]
rs35448554	0.82[ASN][1000 genomes]
rs35585199	0.86[ASN][1000 genomes]
rs3821023	0.95[EUR][1000 genomes]
rs4670262	0.88[ASN][1000 genomes]
rs4670263	0.95[EUR][1000 genomes]
rs4670882	0.93[EUR][1000 genomes]
rs4670883	0.93[EUR][1000 genomes]
rs4670885	0.89[ASN][1000 genomes]
rs58757994	0.89[ASN][1000 genomes]
rs6707543	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732137	0.94[EUR][1000 genomes]
rs6736380	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761563	0.95[EUR][1000 genomes]
rs7571326	0.94[EUR][1000 genomes]
rs7574493	0.93[EUR][1000 genomes]
rs7588762	0.93[EUR][1000 genomes]
rs7590750	0.95[EUR][1000 genomes]
rs7590835	0.95[EUR][1000 genomes]
rs7590926	0.95[EUR][1000 genomes]
rs7597535	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38892600-38893200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:38892600-38893200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:38892600-38893200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:38892600-38893400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:38892600-38893400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:38892600-38893400	Active TSS	Rectal Smooth Muscle	rectum
7	chr2:38892600-38893400	Active TSS	Stomach Smooth Muscle	stomach
8	chr2:38892600-38893600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:38892600-38893600	Active TSS	Fetal Lung	lung
10	chr2:38892600-38893600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr2:38892600-38893800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:38892600-38894000	Active TSS	Fetal Intestine Large	intestine
13	chr2:38892600-38894400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:38892800-38893200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:38892800-38893200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr2:38892800-38893200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:38892800-38893200	Active TSS	Brain Hippocampus Middle	brain
18	chr2:38892800-38893200	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr2:38892800-38893200	Active TSS	HSMM	muscle
20	chr2:38892800-38893200	Active TSS	HUVEC	blood vessel
21	chr2:38892800-38893400	Active TSS	Primary monocytes fromperipheralblood	blood
22	chr2:38892800-38893400	Active TSS	Primary T cells from cord blood	blood
23	chr2:38892800-38893400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:38892800-38893400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr2:38892800-38893400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr2:38892800-38893400	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr2:38892800-38893400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:38892800-38893400	Active TSS	Adipose Nuclei	Adipose
29	chr2:38892800-38893400	Active TSS	Colonic Mucosa	Colon
30	chr2:38892800-38893400	Active TSS	Duodenum Mucosa	Duodenum
31	chr2:38892800-38893400	Active TSS	Fetal Brain Male	brain
32	chr2:38892800-38893400	Active TSS	Fetal Brain Female	brain
33	chr2:38892800-38893400	Active TSS	Fetal Intestine Small	intestine
34	chr2:38892800-38893400	Active TSS	Fetal Muscle Trunk	muscle
35	chr2:38892800-38893400	Active TSS	Fetal Muscle Leg	muscle
36	chr2:38892800-38893400	Active TSS	Left Ventricle	heart
37	chr2:38892800-38893400	Active TSS	HSMMtube	muscle
38	chr2:38892800-38893400	Active TSS	NH-A	brain
39	chr2:38892800-38893600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr2:38892800-38893600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr2:38892800-38893600	Active TSS	Brain Substantia Nigra	brain
42	chr2:38892800-38893600	Active TSS	Fetal Heart	heart
43	chr2:38892800-38893600	Active TSS	A549	lung
44	chr2:38892800-38893600	Active TSS	NHDF-Ad	bronchial
45	chr2:38892800-38893800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr2:38892800-38893800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr2:38892800-38893800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr2:38892800-38893800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:38892800-38893800	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:38892800-38893800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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