Variant report

Variant	rs11555856
Chromosome Location	chr2:54785492-54785493
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	YY1	chr2:54785382-54785959	ECC-1	luminal epithelium:	n/a	chr2:54785508-54785522 chr2:54785504-54785518 chr2:54785505-54785519
2	TAF1	chr2:54784823-54785960	K562	blood:	n/a	n/a
3	BHLHE40	chr2:54784674-54785745	GM12878	blood:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785310-54785326 chr2:54785082-54785098 chr2:54785508-54785524
4	POLR2A	chr2:54784604-54785679	HCT-116	colon:	n/a	n/a
5	MAX	chr2:54784637-54786245	K562	blood:	n/a	chr2:54785854-54785864
6	USF1	chr2:54785264-54785573	H1-hESC	embryonic stem cell:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785446-54785457 chr2:54785310-54785326 chr2:54785508-54785524
7	POLR2A	chr2:54784775-54788123	GM18951	blood:	n/a	n/a
8	EP300	chr2:54785395-54785856	GM12878	blood:	n/a	chr2:54785508-54785524 chr2:54785503-54785512 chr2:54785505-54785521 chr2:54785509-54785525 chr2:54785505-54785514 chr2:54785506-54785522
9	E2F4	chr2:54784672-54786020	K562	blood:	n/a	chr2:54785451-54785460 chr2:54785328-54785338 chr2:54785041-54785051 chr2:54785453-54785462
10	POLR2A	chr2:54785256-54785611	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:54784845-54788076	GM12891	blood:	n/a	n/a
12	ELK1	chr2:54785398-54785836	Hela-S3	cervix:	n/a	n/a
13	BHLHE40	chr2:54784730-54786083	K562	blood:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785310-54785326 chr2:54785082-54785098 chr2:54785508-54785524
14	POLR2A	chr2:54784560-54786389	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr2:54785313-54785735	SK-N-SH	brain:	n/a	n/a
16	MAZ	chr2:54784601-54786029	Hela-S3	cervix:	n/a	chr2:54785854-54785864
17	POLR2A	chr2:54785281-54785948	HUVEC	blood vessel:	n/a	n/a
18	TAF1	chr2:54784688-54786257	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr2:54785255-54786247	GM12878	blood:	n/a	n/a
20	MAX	chr2:54784513-54786134	HepG2	liver:	n/a	chr2:54785854-54785864
21	MAX	chr2:54784741-54785718	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:54784800-54788668	GM19099	blood:	n/a	n/a
23	USF2	chr2:54785222-54785600	H1-hESC	embryonic stem cell:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785310-54785326 chr2:54785508-54785524
24	POLR2A	chr2:54784632-54785877	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr2:54784624-54785772	MCF10A-Er-Src	breast:	n/a	n/a
26	ELF1	chr2:54784805-54786081	GM12878	blood:	n/a	chr2:54785043-54785052 chr2:54785503-54785515 chr2:54785502-54785514
27	CHD2	chr2:54784813-54786380	HepG2	liver:	n/a	n/a
28	TAF1	chr2:54784690-54785840	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr2:54785417-54788004	A549	lung:	n/a	n/a
30	POLR2A	chr2:54784719-54786277	Hela-S3	cervix:	n/a	n/a
31	MYC	chr2:54785360-54785692	K562	blood:	n/a	n/a
32	YY1	chr2:54785226-54785650	H1-hESC	embryonic stem cell:	n/a	chr2:54785331-54785342 chr2:54785508-54785522 chr2:54785504-54785518 chr2:54785320-54785331 chr2:54785505-54785519
33	GATA1	chr2:54785190-54785777	PBDE	blood:	n/a	n/a
34	POLR2A	chr2:54784792-54785628	A549	lung:	n/a	n/a
35	POLR2A	chr2:54784682-54790584	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr2:54785320-54785701	HepG2	liver:	n/a	n/a
37	MXI1	chr2:54784731-54787967	Hela-S3	cervix:	n/a	n/a
38	CBX3	chr2:54785333-54785962	K562	blood:	n/a	n/a
39	YY1	chr2:54785464-54785918	H1-hESC	embryonic stem cell:	n/a	chr2:54785508-54785522 chr2:54785504-54785518 chr2:54785505-54785519
40	RCOR1	chr2:54784652-54785705	K562	blood:	n/a	n/a
41	SP4	chr2:54785342-54785647	H1-hESC	embryonic stem cell:	n/a	n/a
42	NFYB	chr2:54785285-54785641	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:54785375-54785639	K562	blood:	n/a	n/a
44	MAX	chr2:54784423-54786207	HCT-116	colon:	n/a	chr2:54785854-54785864
45	POLR2A	chr2:54784589-54788391	HepG2	liver:	n/a	n/a
46	MYC	chr2:54784763-54785694	K562	blood:	n/a	n/a
47	REST	chr2:54785377-54788021	A549	lung:	n/a	chr2:54786046-54786066 chr2:54786049-54786062 chr2:54785827-54785840 chr2:54785531-54785544 chr2:54786230-54786238 chr2:54785851-54785864
48	USF1	chr2:54785140-54785627	H1-hESC	embryonic stem cell:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785446-54785457 chr2:54785310-54785326 chr2:54785508-54785524
49	ZMIZ1	chr2:54784861-54785990	K562	blood:	n/a	n/a
50	USF1	chr2:54785323-54785760	ECC-1	luminal epithelium:	n/a	chr2:54785503-54785519 chr2:54785446-54785457 chr2:54785508-54785524

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:54785473-54785523	HepG2	liver:	n/a
2	chr2:54785473-54785523	AG09309	skin:	n/a
3	chr2:54785476-54785526	K562	blood:	n/a
4	chr2:54785473-54785523	Hepatocyte	liver:	n/a
5	chr2:54785473-54785523	U87	brain:	n/a
6	chr2:54785473-54785523	HRE	kidney:	n/a
7	chr2:54785473-54785523	AoSMC	blood vessel:	n/a
8	chr2:54785473-54785523	NHDF-neo	bronchial:	n/a
9	chr2:54785476-54785526	A549	lung:	n/a
10	chr2:54785473-54785523	GM12878	blood:	n/a
11	chr2:54785473-54785523	H1-hESC	embryonic stem cell:	embryo
12	chr2:54785473-54785523	AG04450	lung:	fetal
13	chr2:54785473-54785523	HCF	heart:	n/a
14	chr2:54785476-54785526	HUVEC	blood vessel:	n/a
15	chr2:54785476-54785526	ProgFib	skin:	n/a
16	chr2:54785473-54785523	PrEC	prostate:	n/a
17	chr2:54785473-54785523	GM12892	blood:	n/a
18	chr2:54785476-54785526	GM06990	blood:	n/a
19	chr2:54785476-54785526	HepG2	liver:	n/a
20	chr2:54785476-54785526	SK-N-MC	brain:	n/a
21	chr2:54785476-54785526	HRE	kidney:	n/a
22	chr2:54785476-54785526	AG09309	skin:	n/a
23	chr2:54785476-54785526	U87	brain:	n/a
24	chr2:54785473-54785523	ProgFib	skin:	n/a
25	chr2:54785473-54785523	MCF10A-Er-Src	breast:	n/a
26	chr2:54785473-54785523	Jurkat	blood:	n/a
27	chr2:54785476-54785526	PFSK-1	brain:	n/a
28	chr2:54785473-54785523	SKMC	muscle:	n/a
29	chr2:54785473-54785523	RPTEC	kidney:	n/a
30	chr2:54785473-54785523	AG04449	skin:	fetal
31	chr2:54785476-54785526	PANC-1	pancreas:	n/a
32	chr2:54785473-54785523	A549	lung:	n/a
33	chr2:54785476-54785526	NH-A	brain:	n/a
34	chr2:54785473-54785523	HL-60	blood:	n/a
35	chr2:54785476-54785526	BJ	skin:	n/a
36	chr2:54785473-54785523	GM19239	blood:	n/a
37	chr2:54785473-54785523	ECC-1	luminal epithelium:	n/a
38	chr2:54785476-54785526	MCF10A-Er-Src	breast:	n/a
39	chr2:54785476-54785526	PrEC	prostate:	n/a
40	chr2:54785473-54785523	Caco-2	colon:	n/a
41	chr2:54785476-54785526	HIPEpiC	eye:	n/a
42	chr2:54785476-54785526	AG04450	lung:	fetal
43	chr2:54785473-54785523	IMR90	lung:	fetal
44	chr2:54785476-54785526	GM19239	blood:	n/a
45	chr2:54785473-54785523	CMK	blood:	n/a
46	chr2:54785473-54785523	HCT-116	colon:	n/a
47	chr2:54785476-54785526	HNPCEpiC	eye:	n/a
48	chr2:54785473-54785523	BE2_C	brain:	n/a
49	chr2:54785473-54785523	HPAEpiC	pulmonary alveolar:	n/a
50	chr2:54785473-54785523	K562	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:
2	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
3	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:
4	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
5	chr2:54772020..54776106-chr2:54782775..54785505,4	K562	blood:
6	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
7	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
SPTBN1	CpG island
ENSG00000170634	Chromatin interaction
ENSG00000214595	Chromatin interaction
ENSG00000237887	Chromatin interaction
ENSG00000234943	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10176359	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10176445	0.84[ASN][1000 genomes]
rs10183043	0.80[EUR][1000 genomes]
rs10210502	0.83[EUR][1000 genomes]
rs10528	0.87[EUR][1000 genomes]
rs11892236	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11896957	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11902659	0.88[EUR][1000 genomes]
rs11904679	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12713262	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713263	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713270	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713271	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713272	0.88[EUR][1000 genomes]
rs12713273	0.83[EUR][1000 genomes]
rs12987967	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13004944	0.90[EUR][1000 genomes]
rs13021606	0.96[EUR][1000 genomes]
rs13021615	0.85[EUR][1000 genomes]
rs13391803	0.89[EUR][1000 genomes]
rs13408295	0.82[EUR][1000 genomes]
rs17039558	0.91[EUR][1000 genomes]
rs17046036	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17046061	0.85[EUR][1000 genomes]
rs17046067	0.85[EUR][1000 genomes]
rs2229503	0.87[EUR][1000 genomes]
rs34077590	0.91[EUR][1000 genomes]
rs34094680	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34263579	0.83[EUR][1000 genomes]
rs34308676	0.89[EUR][1000 genomes]
rs34311770	0.85[EUR][1000 genomes]
rs34429083	0.81[EUR][1000 genomes]
rs34978408	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35619551	0.84[EUR][1000 genomes]
rs36018286	0.81[EUR][1000 genomes]
rs3796022	0.85[EUR][1000 genomes]
rs4261758	0.86[EUR][1000 genomes]
rs4319969	0.83[EUR][1000 genomes]
rs4358162	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519566	0.84[EUR][1000 genomes]
rs45487791	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577321	0.84[EUR][1000 genomes]
rs57281248	0.91[EUR][1000 genomes]
rs58419243	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61126015	0.89[EUR][1000 genomes]
rs6545430	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545435	0.84[EUR][1000 genomes]
rs66693131	0.85[EUR][1000 genomes]
rs67079536	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6721612	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724136	0.80[EUR][1000 genomes]
rs67244067	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6730876	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6734445	0.87[EUR][1000 genomes]
rs6734536	0.91[EUR][1000 genomes]
rs6740893	0.86[ASN][1000 genomes]
rs6741053	0.92[EUR][1000 genomes]
rs7424459	0.87[EUR][1000 genomes]
rs7569127	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7584223	0.84[EUR][1000 genomes]
rs7586066	0.88[EUR][1000 genomes]
rs7602992	0.84[EUR][1000 genomes]
rs7608414	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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:54782200-54785600	Enhancers	Fetal Heart	heart
2	chr2:54782800-54785600	Enhancers	HSMMtube	muscle
3	chr2:54784000-54788200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54784200-54786200	Enhancers	Fetal Brain Male	brain
5	chr2:54784200-54788400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:54784400-54785600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr2:54784400-54788400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:54784600-54785600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:54784600-54785800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:54784600-54785800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr2:54784600-54785800	Active TSS	Rectal Smooth Muscle	rectum
12	chr2:54784600-54787800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:54784600-54787800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:54784600-54787800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:54784600-54787800	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr2:54784600-54788000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr2:54784600-54788200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:54784600-54788200	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr2:54784600-54788400	Active TSS	Thymus	Thymus
20	chr2:54784600-54788600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:54784600-54788800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:54784800-54785600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:54784800-54785600	Active TSS	Fetal Stomach	stomach
24	chr2:54784800-54785800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:54784800-54785800	Active TSS	Brain Anterior Caudate	brain
26	chr2:54784800-54785800	Active TSS	Colon Smooth Muscle	Colon
27	chr2:54784800-54785800	Active TSS	Placenta	Placenta
28	chr2:54784800-54785800	Active TSS	Ovary	ovary
29	chr2:54784800-54786000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr2:54784800-54786000	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr2:54784800-54786000	Active TSS	A549	lung
32	chr2:54784800-54786200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:54784800-54786200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:54784800-54786400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:54784800-54786400	Active TSS	Aorta	Aorta
36	chr2:54784800-54786400	Flanking Active TSS	Left Ventricle	heart
37	chr2:54784800-54786600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr2:54784800-54786800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:54784800-54787000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:54784800-54787000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:54784800-54787600	Active TSS	Gastric	stomach
42	chr2:54784800-54787800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:54784800-54787800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr2:54784800-54787800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:54784800-54787800	Active TSS	Esophagus	oesophagus
46	chr2:54784800-54788000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr2:54784800-54788000	Active TSS	Liver	Liver
48	chr2:54784800-54788200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:54784800-54788200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:54784800-54788200	Active TSS	Lung	lung

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