Variant report

Variant	rs13391762
Chromosome Location	chr2:54784930-54784931
allele	C/G
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	CTCFL	chr2:54784914-54785140	K562	blood:	n/a	n/a
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	FOXA1	chr2:54784682-54784950	T-47D	breast:	n/a	n/a
7	POLR2A	chr2:54784775-54788123	GM18951	blood:	n/a	n/a
8	MAX	chr2:54784703-54785282	MCF-7	breast:	n/a	n/a
9	E2F4	chr2:54784672-54786020	K562	blood:	n/a	chr2:54785451-54785460 chr2:54785328-54785338 chr2:54785041-54785051 chr2:54785453-54785462
10	FOXA2	chr2:54784667-54785116	A549	lung:	n/a	n/a
11	POLR2A	chr2:54784845-54788076	GM12891	blood:	n/a	n/a
12	BHLHE40	chr2:54784730-54786083	K562	blood:	n/a	chr2:54785503-54785519 chr2:54785318-54785334 chr2:54785310-54785326 chr2:54785082-54785098 chr2:54785508-54785524
13	POLR2A	chr2:54784560-54786389	HepG2	liver:	n/a	n/a
14	MAZ	chr2:54784601-54786029	Hela-S3	cervix:	n/a	chr2:54785854-54785864
15	TAF1	chr2:54784688-54786257	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr2:54784513-54786134	HepG2	liver:	n/a	chr2:54785854-54785864
17	MAX	chr2:54784741-54785718	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:54784780-54784930	HAc	cerebellar:	n/a	n/a
19	SIN3AK20	chr2:54784688-54785064	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:54784800-54788668	GM19099	blood:	n/a	n/a
21	CTCF	chr2:54784820-54784970	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr2:54784632-54785877	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr2:54784624-54785772	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXA1	chr2:54784565-54785097	HepG2	liver:	n/a	n/a
25	ELF1	chr2:54784805-54786081	GM12878	blood:	n/a	chr2:54785043-54785052 chr2:54785503-54785515 chr2:54785502-54785514
26	CHD2	chr2:54784813-54786380	HepG2	liver:	n/a	n/a
27	CTCF	chr2:54784900-54785050	GM12865	blood:	n/a	n/a
28	TAF1	chr2:54784690-54785840	ECC-1	luminal epithelium:	n/a	n/a
29	STAT3	chr2:54784671-54785075	MCF10A-Er-Src	breast:	n/a	chr2:54784890-54784899 chr2:54784889-54784900 chr2:54784736-54784747 chr2:54784721-54784729 chr2:54784891-54784900 chr2:54784888-54784902
30	POLR2A	chr2:54784719-54786277	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr2:54784636-54785192	PANC-1	pancreas:	n/a	n/a
32	CTCF	chr2:54784780-54784930	GM12866	blood:	n/a	n/a
33	CTCF	chr2:54784860-54785010	SAEC	small airway:	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	MXI1	chr2:54784731-54787967	Hela-S3	cervix:	n/a	n/a
37	MTA3	chr2:54784568-54785403	GM12878	blood:	n/a	n/a
38	RCOR1	chr2:54784652-54785705	K562	blood:	n/a	n/a
39	MAX	chr2:54784423-54786207	HCT-116	colon:	n/a	chr2:54785854-54785864
40	POLR2A	chr2:54784589-54788391	HepG2	liver:	n/a	n/a
41	PML	chr2:54784799-54785316	K562	blood:	n/a	n/a
42	CTCF	chr2:54784800-54785070	NB4	blood:	n/a	n/a
43	MYC	chr2:54784763-54785694	K562	blood:	n/a	n/a
44	RUNX3	chr2:54784525-54785230	GM12878	blood:	n/a	n/a
45	FOXA1	chr2:54784534-54785094	HepG2	liver:	n/a	n/a
46	SIN3A	chr2:54784783-54785083	GM12878	blood:	n/a	chr2:54784985-54784998
47	ZMIZ1	chr2:54784861-54785990	K562	blood:	n/a	n/a
48	MAX	chr2:54784825-54786035	NB4	blood:	n/a	chr2:54785854-54785864
49	POLR2A	chr2:54784801-54787825	GM19193	blood:	n/a	n/a
50	CTCF	chr2:54784800-54785223	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
2	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:
3	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
4	chr2:54783297..54785333-chr2:54809031..54810704,2	K562	blood:
5	chr2:54772020..54776106-chr2:54782775..54785505,4	K562	blood:
6	chr12:57913784..57914554-chr2:54784859..54785443,2	Hela-S3	cervix:
7	chr2:54784518..54785239-chr6:26205064..26205760,2	Hela-S3	cervix:
8	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
9	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000237887	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000234943	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10169013	1.00[ASN][1000 genomes]
rs10171393	1.00[ASN][1000 genomes]
rs10172671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182310	1.00[ASN][1000 genomes]
rs10188548	1.00[ASN][1000 genomes]
rs10189084	1.00[ASN][1000 genomes]
rs10191357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194488	1.00[ASN][1000 genomes]
rs10195423	1.00[ASN][1000 genomes]
rs10206622	1.00[ASN][1000 genomes]
rs13403817	1.00[ASN][1000 genomes]
rs13414727	1.00[ASN][1000 genomes]
rs13415413	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423872	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13425620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426037	1.00[ASN][1000 genomes]
rs13427468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431302	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17045949	1.00[ASN][1000 genomes]
rs2229505	1.00[ASN][1000 genomes]
rs28496426	1.00[ASN][1000 genomes]
rs28609649	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660202	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28679552	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4387841	1.00[ASN][1000 genomes]
rs6545417	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545426	1.00[ASN][1000 genomes]
rs6735962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746379	1.00[ASN][1000 genomes]
rs7340250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934326	1.00[ASN][1000 genomes]
rs7574433	1.00[ASN][1000 genomes]
rs9808516	1.00[EUR][1000 genomes];1.00[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	chr2:54782600-54785000	Enhancers	Brain Angular Gyrus	brain
3	chr2:54782800-54785000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr2:54782800-54785200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:54782800-54785600	Enhancers	HSMMtube	muscle
6	chr2:54784000-54785000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:54784000-54785000	Flanking Active TSS	Hela-S3	cervix
8	chr2:54784000-54785000	Flanking Active TSS	Osteobl	bone
9	chr2:54784000-54788200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr2:54784200-54785000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:54784200-54785000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:54784200-54785000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:54784200-54785000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:54784200-54785000	Flanking Active TSS	Fetal Kidney	kidney
15	chr2:54784200-54785000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr2:54784200-54785000	Flanking Active TSS	GM12878-XiMat	blood
17	chr2:54784200-54786200	Enhancers	Fetal Brain Male	brain
18	chr2:54784200-54788400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:54784400-54785000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:54784400-54785000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr2:54784400-54785000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:54784400-54785000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:54784400-54785000	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr2:54784400-54785000	Weak transcription	Small Intestine	intestine
25	chr2:54784400-54785000	Flanking Active TSS	NHEK	skin
26	chr2:54784400-54785200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr2:54784400-54785400	Flanking Active TSS	NH-A	brain
28	chr2:54784400-54785600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr2:54784400-54788400	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:54784600-54785000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:54784600-54785000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr2:54784600-54785000	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr2:54784600-54785000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr2:54784600-54785000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:54784600-54785000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:54784600-54785000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:54784600-54785000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:54784600-54785000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr2:54784600-54785000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:54784600-54785000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr2:54784600-54785000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr2:54784600-54785000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:54784600-54785000	Flanking Active TSS	Colonic Mucosa	Colon
44	chr2:54784600-54785000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr2:54784600-54785000	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr2:54784600-54785000	Flanking Active TSS	Fetal Lung	lung
47	chr2:54784600-54785000	Flanking Active TSS	Fetal Thymus	thymus
48	chr2:54784600-54785000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr2:54784600-54785000	Flanking Active TSS	HUVEC	blood vessel
50	chr2:54784600-54785000	Flanking Active TSS	K562	blood

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