Variant report

Variant	rs13386539
Chromosome Location	chr2:85978008-85978009
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	MAX	chr2:85977685-85978773	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr2:85977543-85978104	HepG2	liver:	n/a	chr2:85977801-85977820
3	CREB1	chr2:85977691-85978065	A549	lung:	n/a	n/a
4	CTCF	chr2:85977505-85978064	A549	lung:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
5	SIX5	chr2:85977497-85978288	A549	lung:	n/a	n/a
6	CTCF	chr2:85977677-85978099	K562	blood:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
7	RAD21	chr2:85977551-85978049	SK-N-SH_RA	brain:	n/a	chr2:85977801-85977820
8	RAD21	chr2:85977535-85978092	A549	lung:	n/a	chr2:85977801-85977820
9	RAD21	chr2:85977538-85978048	ECC-1	luminal epithelium:	n/a	chr2:85977801-85977820
10	RAD21	chr2:85977514-85978201	ECC-1	luminal epithelium:	n/a	chr2:85977801-85977820
11	RAD21	chr2:85977185-85978407	SK-N-SH	brain:	n/a	chr2:85977801-85977820
12	CTCF	chr2:85977317-85978207	HCT-116	colon:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
13	MAFK	chr2:85977762-85978014	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr2:85977587-85978243	Hela-S3	cervix:	n/a	chr2:85977802-85977810 chr2:85977802-85977816
15	SMC3	chr2:85977504-85978019	HepG2	liver:	n/a	chr2:85977802-85977810 chr2:85977802-85977816
16	RAD21	chr2:85977505-85978053	H1-hESC	embryonic stem cell:	n/a	chr2:85977801-85977820
17	RAD21	chr2:85977476-85978219	HCT-116	colon:	n/a	chr2:85977801-85977820
18	RAD21	chr2:85977569-85978057	HepG2	liver:	n/a	chr2:85977801-85977820
19	CTCF	chr2:85977409-85978141	HCT-116	colon:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
20	CTCF	chr2:85977587-85978012	A549	lung:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
21	RAD21	chr2:85977533-85978188	MCF-7	breast:	n/a	chr2:85977801-85977820
22	CTCF	chr2:85977289-85978286	SK-N-SH	brain:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
23	CTCF	chr2:85977502-85978072	MCF-7	breast:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
24	CTCF	chr2:85977248-85978410	A549	lung:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
25	CTCF	chr2:85977559-85978076	MCF-7	breast:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
26	RAD21	chr2:85977415-85978272	HCT-116	colon:	n/a	chr2:85977801-85977820
27	SIN3AK20	chr2:85977536-85978038	A549	lung:	n/a	n/a
28	SPI1	chr2:85977554-85978081	HL-60	blood:	n/a	chr2:85977752-85977761
29	CTCF	chr2:85977604-85978015	A549	lung:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
30	NRF1	chr2:85977996-85978027	GM12878	blood:	n/a	n/a
31	SMC3	chr2:85977297-85978602	SK-N-SH	brain:	n/a	chr2:85977802-85977810 chr2:85977802-85977816
32	CTCF	chr2:85977564-85978037	H1-hESC	embryonic stem cell:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818
33	RAD21	chr2:85977498-85978118	MCF-7	breast:	n/a	chr2:85977801-85977820
34	RAD21	chr2:85977598-85978097	HepG2	liver:	n/a	chr2:85977801-85977820
35	RAD21	chr2:85977609-85978025	Hela-S3	cervix:	n/a	chr2:85977801-85977820
36	RAD21	chr2:85977621-85978031	A549	lung:	n/a	chr2:85977801-85977820
37	TCF12	chr2:85977318-85978427	A549	lung:	n/a	chr2:85978299-85978309 chr2:85977820-85977830
38	ZNF263	chr2:85977614-85978108	HEK293-T-REx	kidney:	n/a	chr2:85977852-85977873
39	NFIC	chr2:85977925-85978424	ECC-1	luminal epithelium:	n/a	chr2:85978385-85978401 chr2:85978384-85978401
40	RAD21	chr2:85977583-85978026	IMR90	lung:	n/a	chr2:85977801-85977820
41	RAD21	chr2:85977428-85978236	A549	lung:	n/a	chr2:85977801-85977820
42	RAD21	chr2:85977605-85978012	H1-hESC	embryonic stem cell:	n/a	chr2:85977801-85977820
43	CTCF	chr2:85977678-85978022	K562	blood:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818

No.	Distal block	Cell Line	Cell type
1	chr2:85976745..85979342-chr2:85979775..85983018,3	K562	blood:
2	chr2:85977766..85978267-chr2:86041056..86041985,2	K562	blood:
3	chr2:85971643..85974209-chr2:85976098..85978084,3	MCF-7	breast:
4	chr2:85977427..85978425-chr2:86024880..86025694,8	MCF-7	breast:
5	chr2:85955784..85956751-chr2:85977453..85978247,3	MCF-7	breast:
6	chr2:85977304..85978300-chr2:86041004..86041953,11	MCF-7	breast:
7	chr2:85977326..85978260-chr2:86024538..86025326,2	MCF-7	breast:
8	chr2:85977777..85978300-chr2:85999453..86000129,2	MCF-7	breast:
9	chr2:85977362..85978288-chr2:86031431..86032387,4	K562	blood:
10	chr2:85976672..85979342-chr2:85979775..85983871,4	K562	blood:

Variant related genes	Relation type
ATOH8	TF binding region
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10175441	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10176095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402756	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13418020	0.85[EUR][1000 genomes]
rs13431188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2118400	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85972400-85978200	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:85973000-85979000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:85973400-85980200	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr2:85974800-85980400	Enhancers	Fetal Heart	heart
5	chr2:85975200-85979400	Enhancers	Fetal Lung	lung
6	chr2:85975600-85979800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:85975600-85980000	Enhancers	Brain Substantia Nigra	brain
8	chr2:85975800-85978800	Enhancers	Hela-S3	cervix
9	chr2:85975800-85979600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:85975800-85980000	Enhancers	HSMM	muscle
11	chr2:85975800-85980400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:85976000-85978600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:85976000-85978800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:85976000-85979600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:85976000-85979800	Enhancers	Brain Hippocampus Middle	brain
16	chr2:85976000-85979800	Enhancers	A549	lung
17	chr2:85976600-85979000	Enhancers	HSMMtube	muscle
18	chr2:85976600-85980200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:85976800-85978200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:85976800-85978200	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:85976800-85979000	Enhancers	Colon Smooth Muscle	Colon
22	chr2:85977000-85980000	Weak transcription	Gastric	stomach
23	chr2:85977000-85980200	Weak transcription	Aorta	Aorta
24	chr2:85977400-85980000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:85977600-85978600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:85977600-85978600	Enhancers	Psoas Muscle	Psoas
27	chr2:85977600-85978600	Enhancers	Osteobl	bone
28	chr2:85977600-85978800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:85977600-85979000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:85977600-85979000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:85977600-85979400	Enhancers	NHDF-Ad	bronchial
32	chr2:85977600-85980200	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:85977600-85980200	Enhancers	Left Ventricle	heart
34	chr2:85977600-85980200	Enhancers	Right Ventricle	heart
35	chr2:85977600-85980400	Enhancers	Lung	lung
36	chr2:85977600-85980800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:85977800-85978200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
38	chr2:85977800-85978200	Enhancers	Small Intestine	intestine
39	chr2:85977800-85978200	Enhancers	Stomach Mucosa	stomach
40	chr2:85977800-85978400	Bivalent Enhancer	Rectal Smooth Muscle	rectum
41	chr2:85977800-85978600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
42	chr2:85977800-85978800	Enhancers	Esophagus	oesophagus
43	chr2:85977800-85978800	Enhancers	Pancreas	Pancrea
44	chr2:85977800-85979200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:85977800-85979200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:85977800-85979200	Bivalent Enhancer	Placenta	Placenta
47	chr2:85977800-85979200	Enhancers	NHLF	lung
48	chr2:85977800-85979400	Bivalent Enhancer	Fetal Stomach	stomach
49	chr2:85977800-85979600	Enhancers	Right Atrium	heart
50	chr2:85977800-85979600	Enhancers	Spleen	Spleen

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