Variant report

Variant	rs62109427
Chromosome Location	chr2:20215481-20215482
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	ARID3A	chr2:20215262-20215641	HepG2	liver:	n/a	n/a
2	RAD21	chr2:20215257-20215684	Hela-S3	cervix:	n/a	chr2:20215430-20215449
3	CTCF	chr2:20215400-20215550	HVMF	connective:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
4	EP300	chr2:20215359-20215559	K562	blood:	n/a	n/a
5	CTCF	chr2:20215360-20215510	Caco-2	colon:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
6	CTCF	chr2:20215340-20215490	HMF	breast:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
7	CTCF	chr2:20215271-20215678	HepG2	liver:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
8	RFX5	chr2:20215317-20215598	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr2:20215424-20215519	ProgFib	skin:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
10	CTCF	chr2:20215253-20215651	K562	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
11	CTCF	chr2:20215380-20215530	GM12864	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
12	CTCF	chr2:20215400-20215550	GM12871	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
13	CTCF	chr2:20215350-20215548	HepG2	liver:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
14	CTCF	chr2:20215380-20215530	AG10803	skin:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
15	RAD21	chr2:20215140-20215788	HCT-116	colon:	n/a	chr2:20215430-20215449
16	CTCF	chr2:20215217-20215608	A549	lung:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
17	CTCF	chr2:20215328-20215548	GM13977	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
18	CTCF	chr2:20215340-20215490	HA-sp	spinal cord:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
19	RAD21	chr2:20215293-20215620	A549	lung:	n/a	chr2:20215430-20215449
20	CTCF	chr2:20215380-20215530	GM12801	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
21	RAD21	chr2:20215215-20215593	H1-hESC	embryonic stem cell:	n/a	chr2:20215430-20215449
22	CTCF	chr2:20215360-20215510	HPAF	blood vessel:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
23	RAD21	chr2:20215198-20215703	SK-N-SH_RA	brain:	n/a	chr2:20215430-20215449
24	CTCF	chr2:20215380-20215530	Caco-2	colon:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
25	CTCF	chr2:20215259-20215611	ECC-1	luminal epithelium:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
26	CTCF	chr2:20215380-20215530	NHDF-neo	bronchial:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
27	CTCF	chr2:20215380-20215530	HMEC	breast:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
28	CTCF	chr2:20215195-20215631	HCT-116	colon:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
29	CTCF	chr2:20215312-20215550	GM10266	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
30	RAD21	chr2:20215235-20215583	GM12878	blood:	n/a	chr2:20215430-20215449
31	CTCF	chr2:20215360-20215510	AG04450	lung:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
32	CTCF	chr2:20215360-20215510	HEK293	kidney:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
33	CTCF	chr2:20215254-20215585	A549	lung:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
34	CTCF	chr2:20215400-20215550	AG09309	skin:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
35	CTCF	chr2:20215360-20215510	AG09319	gingival:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
36	CTCF	chr2:20215360-20215510	HRPEpiC	eye:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
37	CTCF	chr2:20215181-20215723	HepG2	liver:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
38	CTCF	chr2:20215338-20215519	LNCaP	prostate:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
39	CTCF	chr2:20215340-20215490	HRE	kidney:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
40	SMC3	chr2:20215079-20215848	SK-N-SH	brain:	n/a	chr2:20215431-20215445
41	E2F4	chr2:20215276-20215516	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr2:20215380-20215530	AG04449	skin:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
43	ZNF384	chr2:20215295-20215541	K562	blood:	n/a	n/a
44	CTCF	chr2:20215305-20215587	Medullo	brain:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
45	CTCF	chr2:20215340-20215490	SK-N-SH_RA	brain:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
46	CTCF	chr2:20215360-20215510	HPF	lung:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
47	CTCF	chr2:20215360-20215510	GM12868	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
48	CTCF	chr2:20215360-20215510	BE2_C	brain:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447
49	ZNF143	chr2:20215312-20215599	K562	blood:	n/a	n/a
50	CTCF	chr2:20215340-20215490	GM06990	blood:	n/a	chr2:20215431-20215452 chr2:20215432-20215445 chr2:20215430-20215446 chr2:20215429-20215447

No.	Distal block	Cell Line	Cell type
1	chr2:20214554..20219540-chr2:20268505..20271599,4	MCF-7	breast:
2	chr2:20155282..20156235-chr2:20215355..20216756,5	MCF-7	breast:
3	chr2:20215373..20215907-chr2:20276846..20277471,2	MCF-7	breast:
4	chr2:20214992..20215965-chr2:20292746..20293998,6	K562	blood:
5	chr2:20215034..20215891-chr2:20293118..20294150,7	MCF-7	breast:
6	chr2:20212101..20214249-chr2:20214270..20216382,2	K562	blood:
7	chr2:20213367..20215755-chr2:20296083..20298973,4	MCF-7	breast:
8	chr2:20205089..20207938-chr2:20214962..20217155,2	MCF-7	breast:
9	chr2:20213655..20215850-chr2:20273111..20274656,2	MCF-7	breast:
10	chr2:20215025..20216011-chr2:20297649..20298217,2	MCF-7	breast:
11	chr2:20214925..20217152-chr2:20292879..20295056,3	MCF-7	breast:
12	chr2:20215401..20215928-chr2:20490512..20491468,2	K562	blood:
13	chr2:20214859..20216804-chr2:20293145..20294071,9	MCF-7	breast:
14	chr2:20214302..20217183-chr2:20301641..20303761,2	MCF-7	breast:
15	chr2:20214958..20215898-chr2:20297637..20298521,4	K562	blood:
16	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
17	chr2:20214721..20216712-chr2:20262631..20264995,2	K562	blood:

Variant related genes	Relation type
MATN3	TF binding region
ENSG00000132031	Chromatin interaction
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11674251	0.93[ASN][1000 genomes]
rs11689431	0.98[ASN][1000 genomes]
rs12988954	0.92[ASN][1000 genomes]
rs34539547	0.86[ASN][1000 genomes]
rs3731667	0.86[AMR][1000 genomes]
rs62109431	0.86[ASN][1000 genomes]
rs6734005	0.86[AMR][1000 genomes]
rs7570360	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20212800-20216200	Weak transcription	HMEC	breast
2	chr2:20213000-20216200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20213000-20218400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:20213000-20220600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:20213000-20227200	Weak transcription	Ovary	ovary
6	chr2:20213200-20217000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:20213200-20218400	Weak transcription	Fetal Heart	heart
8	chr2:20213200-20225000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:20213200-20227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:20213200-20227000	Weak transcription	Aorta	Aorta
11	chr2:20213400-20227400	Weak transcription	Fetal Kidney	kidney
12	chr2:20213400-20232200	Weak transcription	Right Ventricle	heart
13	chr2:20213600-20216600	Enhancers	HepG2	liver
14	chr2:20213600-20227000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:20214800-20220200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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