Variant report

Variant	rs56229257
Chromosome Location	chr2:152685113-152685114
allele	A/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	REST	chr2:152684869-152685272	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr2:152684710-152685386	PFSK-1	brain:	n/a	n/a
3	TAF1	chr2:152684777-152685325	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr2:152684988-152685560	K562	blood:	n/a	n/a
5	TBP	chr2:152684062-152685508	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr2:152684724-152685433	K562	blood:	n/a	n/a
7	POLR2A	chr2:152684025-152685467	GM18526	blood:	n/a	n/a
8	POU2F2	chr2:152684695-152685491	GM12878	blood:	n/a	chr2:152685103-152685114 chr2:152685100-152685113 chr2:152685099-152685117 chr2:152685102-152685112 chr2:152685102-152685112 chr2:152685103-152685112 chr2:152685104-152685112 chr2:152685101-152685115 chr2:152685100-152685115 chr2:152685103-152685113 chr2:152685101-152685113 chr2:152685098-152685119 chr2:152685104-152685111
9	POLR2A	chr2:152684477-152685473	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr2:152684146-152685465	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr2:152684672-152685285	A549	lung:	n/a	n/a
12	CREB1	chr2:152684707-152685442	H1-hESC	embryonic stem cell:	n/a	chr2:152685316-152685329
13	HCFC1	chr2:152684225-152685571	K562	blood:	n/a	n/a
14	REST	chr2:152685061-152685383	A549	lung:	n/a	n/a
15	MAX	chr2:152684712-152685308	HepG2	liver:	n/a	chr2:152685001-152685011
16	TBL1XR1	chr2:152683333-152685451	K562	blood:	n/a	n/a
17	JUND	chr2:152684688-152685202	A549	lung:	n/a	n/a
18	YY1	chr2:152685049-152685359	GM12892	blood:	n/a	n/a
19	UBTF	chr2:152684066-152685429	K562	blood:	n/a	n/a
20	REST	chr2:152684794-152685236	ECC-1	luminal epithelium:	n/a	n/a
21	ZNF143	chr2:152684249-152685401	H1-hESC	embryonic stem cell:	n/a	chr2:152685001-152685011
22	TBP	chr2:152684069-152685559	K562	blood:	n/a	n/a
23	E2F4	chr2:152684150-152685393	K562	blood:	n/a	chr2:152685077-152685091 chr2:152684535-152684545 chr2:152685001-152685010 chr2:152685044-152685053
24	EGR1	chr2:152684398-152685462	K562	blood:	n/a	chr2:152684551-152684564 chr2:152685044-152685053
25	TBP	chr2:152684240-152685466	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr2:152684638-152685249	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr2:152683986-152685415	H1-neurons	neurons:	n/a	n/a
28	ELK1	chr2:152684734-152685360	GM12878	blood:	n/a	n/a
29	REST	chr2:152683787-152685304	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr2:152684723-152685653	GM12878	blood:	n/a	n/a
31	MAFK	chr2:152684909-152685833	Hela-S3	cervix:	n/a	chr2:152685674-152685689 chr2:152685677-152685691 chr2:152685669-152685689
32	HNF4A	chr2:152684704-152685373	HepG2	liver:	n/a	chr2:152685192-152685200 chr2:152685131-152685146 chr2:152685131-152685146
33	TAF1	chr2:152685023-152685248	Hela-S3	cervix:	n/a	n/a
34	YY1	chr2:152684721-152685320	SK-N-SH_RA	brain:	n/a	n/a
35	POU2F2	chr2:152684755-152685416	GM12878	blood:	n/a	chr2:152685103-152685114 chr2:152685100-152685113 chr2:152685099-152685117 chr2:152685102-152685112 chr2:152685102-152685112 chr2:152685103-152685112 chr2:152685104-152685112 chr2:152685101-152685115 chr2:152685100-152685115 chr2:152685103-152685113 chr2:152685101-152685113 chr2:152685098-152685119 chr2:152685104-152685111
36	TAF1	chr2:152684378-152685345	H1-hESC	embryonic stem cell:	n/a	n/a
37	TEAD4	chr2:152684646-152685556	HepG2	liver:	n/a	n/a
38	MEF2A	chr2:152684671-152685580	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:152684712-152685401	SK-N-SH	brain:	n/a	n/a
40	EP300	chr2:152684752-152685438	HepG2	liver:	n/a	n/a
41	WRNIP1	chr2:152684795-152685586	GM12878	blood:	n/a	n/a
42	MAX	chr2:152684619-152685442	K562	blood:	n/a	chr2:152685001-152685011
43	FOXA1	chr2:152684939-152685264	T-47D	breast:	n/a	n/a
44	EP300	chr2:152684971-152685552	GM12878	blood:	n/a	n/a
45	MAX	chr2:152684764-152685390	SK-N-SH	brain:	n/a	chr2:152685001-152685011
46	POU2F2	chr2:152684606-152685449	GM12891	blood:	n/a	chr2:152685103-152685114 chr2:152685100-152685113 chr2:152685099-152685117 chr2:152685102-152685112 chr2:152685102-152685112 chr2:152685103-152685112 chr2:152685104-152685112 chr2:152685101-152685115 chr2:152685100-152685115 chr2:152685103-152685113 chr2:152685101-152685113 chr2:152685098-152685119 chr2:152685104-152685111
47	RCOR1	chr2:152684716-152685304	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:152684102-152685589	GM19193	blood:	n/a	n/a
49	POLR2A	chr2:152684592-152685454	ECC-1	luminal epithelium:	n/a	n/a
50	ZBTB7A	chr2:152684398-152685125	K562	blood:	n/a	chr2:152685017-152685024

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:152685072-152685122	HCT-116	colon:	n/a
2	chr2:152685072-152685122	Hela-S3	cervix:	n/a
3	chr2:152685072-152685122	HNPCEpiC	eye:	n/a
4	chr2:152685072-152685122	NH-A	brain:	n/a
5	chr2:152685072-152685122	HCM	heart:	n/a
6	chr2:152685088-152685138	T-47D	breast:	n/a
7	chr2:152685072-152685122	HIPEpiC	eye:	n/a
8	chr2:152685072-152685122	HL-60	blood:	n/a
9	chr2:152685072-152685122	HEK293	kidney:	embryo
10	chr2:152685072-152685122	GM06990	blood:	n/a
11	chr2:152685072-152685122	NT2-D1	testis:	n/a
12	chr2:152685088-152685138	CMK	blood:	n/a
13	chr2:152685088-152685138	HCT-116	colon:	n/a
14	chr2:152685072-152685122	SK-N-SH	brain:	n/a
15	chr2:152685072-152685122	HPAEpiC	pulmonary alveolar:	n/a
16	chr2:152685088-152685138	HCM	heart:	n/a
17	chr2:152685072-152685122	HepG2	liver:	n/a
18	chr2:152685072-152685122	HRPEpiC	eye:	n/a
19	chr2:152685072-152685122	RPTEC	kidney:	n/a
20	chr2:152685072-152685122	PANC-1	pancreas:	n/a
21	chr2:152685088-152685138	HIPEpiC	eye:	n/a
22	chr2:152685088-152685138	HRE	kidney:	n/a
23	chr2:152685088-152685138	PFSK-1	brain:	n/a
24	chr2:152685072-152685122	ECC-1	luminal epithelium:	n/a
25	chr2:152685072-152685122	AG04450	lung:	fetal
26	chr2:152685088-152685138	A549	lung:	n/a
27	chr2:152685088-152685138	HNPCEpiC	eye:	n/a
28	chr2:152685072-152685122	AG10803	skin:	n/a
29	chr2:152685072-152685122	HUVEC	blood vessel:	n/a
30	chr2:152685072-152685122	AoSMC	blood vessel:	n/a
31	chr2:152685072-152685122	GM19239	blood:	n/a
32	chr2:152685072-152685122	U87	brain:	n/a
33	chr2:152685072-152685122	HRCEpiC	kidney:	n/a
34	chr2:152685088-152685138	LNCaP	prostate:	n/a
35	chr2:152685072-152685122	IMR90	lung:	fetal
36	chr2:152685088-152685138	ProgFib	skin:	n/a
37	chr2:152685088-152685138	AG09319	gingival:	n/a
38	chr2:152685088-152685138	HCF	heart:	n/a
39	chr2:152685088-152685138	HL-60	blood:	n/a
40	chr2:152685072-152685122	SK-N-MC	brain:	n/a
41	chr2:152685072-152685122	BE2_C	brain:	n/a
42	chr2:152685072-152685122	NHBE	bronchial:	n/a
43	chr2:152685072-152685122	H1-hESC	embryonic stem cell:	embryo
44	chr2:152685088-152685138	K562	blood:	n/a
45	chr2:152685088-152685138	HUVEC	blood vessel:	n/a
46	chr2:152685088-152685138	AG04450	lung:	fetal
47	chr2:152685088-152685138	HepG2	liver:	n/a
48	chr2:152685072-152685122	ovcar-3	ovarian:	n/a
49	chr2:152685072-152685122	AG04449	skin:	fetal
50	chr2:152685088-152685138	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:152684763..152686807-chr2:153031833..153033553,2	MCF-7	breast:
2	chr2:152684655..152685322-chr2:208490382..208491243,2	Hela-S3	cervix:
3	chr2:152685053..152687897-chr2:152732170..152734670,2	K562	blood:

Variant related genes	Relation type
ARL5A	TF binding region
ARL5A	CpG island
ENSG00000115145	Chromatin interaction
ENSG00000144401	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10167462	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1054883	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683122	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683683	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1357468	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1523180	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1799	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2344733	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4267505	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4273217	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7567785	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7596744	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9789671	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 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	chr2:152682800-152685200	Active TSS	Fetal Intestine Large	intestine
2	chr2:152682800-152685200	Active TSS	GM12878-XiMat	blood
3	chr2:152682800-152685200	Active TSS	HMEC	breast
4	chr2:152682800-152685400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:152682800-152685400	Active TSS	Aorta	Aorta
6	chr2:152682800-152685600	Active TSS	Right Atrium	heart
7	chr2:152683000-152685200	Active TSS	Fetal Intestine Small	intestine
8	chr2:152683000-152685600	Active TSS	NHLF	lung
9	chr2:152683000-152685800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:152683200-152685200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:152683200-152685200	Active TSS	Placenta	Placenta
12	chr2:152683200-152685200	Active TSS	HSMM	muscle
13	chr2:152683200-152685400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr2:152683200-152685400	Active TSS	Left Ventricle	heart
15	chr2:152683200-152685600	Active TSS	Ovary	ovary
16	chr2:152683400-152685200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:152683400-152685200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:152683400-152685400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:152683400-152685400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:152683400-152685400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:152683400-152685400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:152683400-152685400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:152683400-152685400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:152683400-152685400	Active TSS	Colonic Mucosa	Colon
25	chr2:152683400-152685600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:152683400-152685600	Active TSS	Psoas Muscle	Psoas
27	chr2:152683600-152685200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:152683600-152685200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:152683600-152685200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:152683600-152685200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:152683600-152685200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:152683600-152685200	Active TSS	Fetal Thymus	thymus
33	chr2:152683600-152685200	Active TSS	Thymus	Thymus
34	chr2:152683600-152685200	Active TSS	HSMMtube	muscle
35	chr2:152683600-152685400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:152683600-152685400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:152683600-152685400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr2:152683600-152685400	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr2:152683600-152685400	Active TSS	Fetal Stomach	stomach
40	chr2:152683600-152685400	Active TSS	Stomach Mucosa	stomach
41	chr2:152683600-152685600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr2:152683600-152685600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:152683600-152685600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:152683600-152685600	Active TSS	Fetal Brain Female	brain
45	chr2:152683600-152685600	Active TSS	Right Ventricle	heart
46	chr2:152683800-152685200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr2:152683800-152685200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:152683800-152685200	Active TSS	Brain Substantia Nigra	brain
49	chr2:152683800-152685200	Active TSS	Fetal Heart	heart
50	chr2:152683800-152685200	Active TSS	Fetal Muscle Leg	muscle

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