Variant report

Variant	rs62260855
Chromosome Location	chr3:48132202-48132203
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48131776-48132521	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48132194-48132244	BE2_C	brain:	n/a
2	chr3:48132194-48132244	HL-60	blood:	n/a
3	chr3:48132194-48132244	HMEC	breast:	n/a
4	chr3:48132194-48132244	MCF-7	breast:	n/a
5	chr3:48132194-48132244	T-47D	breast:	n/a
6	chr3:48132194-48132244	Hela-S3	cervix:	n/a
7	chr3:48132194-48132244	Jurkat	blood:	n/a
8	chr3:48132194-48132244	BJ	skin:	n/a
9	chr3:48132194-48132244	PrEC	prostate:	n/a
10	chr3:48132194-48132244	SKMC	muscle:	n/a
11	chr3:48132194-48132244	GM12892	blood:	n/a
12	chr3:48132194-48132244	GM12878	blood:	n/a
13	chr3:48132194-48132244	SAEC	small airway:	n/a
14	chr3:48132194-48132244	NT2-D1	testis:	n/a
15	chr3:48132194-48132244	HEEpiC	esophagus:	n/a
16	chr3:48132194-48132244	ECC-1	luminal epithelium:	n/a
17	chr3:48132194-48132244	GM19239	blood:	n/a
18	chr3:48132194-48132244	SK-N-SH	brain:	n/a
19	chr3:48132194-48132244	A549	lung:	n/a
20	chr3:48132194-48132244	LNCaP	prostate:	n/a
21	chr3:48132194-48132244	HRCEpiC	kidney:	n/a
22	chr3:48132194-48132244	H1-hESC	embryonic stem cell:	embryo
23	chr3:48132194-48132244	ProgFib	skin:	n/a
24	chr3:48132194-48132244	HCM	heart:	n/a
25	chr3:48132194-48132244	HRE	kidney:	n/a
26	chr3:48132194-48132244	SK-N-MC	brain:	n/a
27	chr3:48132194-48132244	AG10803	skin:	n/a
28	chr3:48132194-48132244	HAEpiC	amniotic membrane:	n/a
29	chr3:48132194-48132244	AG04450	lung:	fetal
30	chr3:48132194-48132244	HEK293	kidney:	embryo
31	chr3:48132194-48132244	HCPEpiC	choroid plexus:	n/a
32	chr3:48132194-48132244	HRPEpiC	eye:	n/a
33	chr3:48132194-48132244	GM06990	blood:	n/a
34	chr3:48132194-48132244	NHBE	bronchial:	n/a
35	chr3:48132194-48132244	AG09309	skin:	n/a
36	chr3:48132194-48132244	K562	blood:	n/a
37	chr3:48132194-48132244	Caco-2	colon:	n/a
38	chr3:48132194-48132244	SK-N-SH_RA	brain:	n/a
39	chr3:48132194-48132244	GM12891	blood:	n/a
40	chr3:48132194-48132244	RPTEC	kidney:	n/a
41	chr3:48132194-48132244	IMR90	lung:	fetal
42	chr3:48132194-48132244	U87	brain:	n/a
43	chr3:48132194-48132244	Hepatocyte	liver:	n/a
44	chr3:48132194-48132244	HCF	heart:	n/a
45	chr3:48132194-48132244	AG04449	skin:	fetal
46	chr3:48132194-48132244	MCF10A-Er-Src	breast:	n/a
47	chr3:48132194-48132244	HPAEpiC	pulmonary alveolar:	n/a
48	chr3:48132194-48132244	NHDF-neo	bronchial:	n/a
49	chr3:48132194-48132244	NB4	blood:	n/a
50	chr3:48132194-48132244	HCT-116	colon:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48130893..48133841-chr3:48154652..48156153,2	K562	blood:
2	chr3:48129047..48133145-chr3:48133622..48137667,6	K562	blood:
3	chr3:48131661..48133215-chr3:48198051..48201016,2	K562	blood:
4	chr3:48129713..48132114-chr3:48132198..48135515,4	MCF-7	breast:
5	chr3:48129047..48133145-chr3:48133826..48138274,6	K562	blood:
6	chr3:47843334..47845793-chr3:48129706..48132338,2	K562	blood:
7	chr3:47843334..47845793-chr3:48129178..48132338,3	K562	blood:
8	chr3:48132094..48133993-chr3:48142496..48145069,2	K562	blood:

No data

Variant related genes	Relation type
MAP4	TF binding region
MAP4	CpG island
ENSG00000047849	Chromatin interaction
ENSG00000265078	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3731544	1.00[ASN][1000 genomes]
rs3731553	1.00[ASN][1000 genomes]
rs62260762	1.00[ASN][1000 genomes]
rs62260779	1.00[ASN][1000 genomes]
rs62260785	1.00[ASN][1000 genomes]
rs62260788	1.00[ASN][1000 genomes]
rs62260850	1.00[ASN][1000 genomes]
rs62263023	1.00[ASN][1000 genomes]
rs62263027	1.00[ASN][1000 genomes]
rs62263577	1.00[ASN][1000 genomes]
rs7638388	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48131800-48132400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:48131800-48133600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:48132000-48132400	Enhancers	Placenta	Placenta
4	chr3:48132000-48133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:48132000-48133800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:48132000-48133800	Weak transcription	K562	blood
7	chr3:48132000-48142000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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