Variant report

Variant	rs62278055
Chromosome Location	chr3:160938811-160938812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:282)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:282 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:160938543-160939291	Hela-S3	cervix:	n/a	n/a
2	YY1	chr3:160938770-160939580	GM12891	blood:	n/a	chr3:160939248-160939262
3	RCOR1	chr3:160938751-160939256	K562	blood:	n/a	n/a
4	POLR2A	chr3:160938734-160939573	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr3:160938327-160939653	MCF-7	breast:	n/a	n/a
6	RFX5	chr3:160938707-160939291	HepG2	liver:	n/a	n/a
7	YY1	chr3:160938772-160939449	GM12878	blood:	n/a	chr3:160939248-160939262
8	MAFK	chr3:160938801-160939168	K562	blood:	n/a	n/a
9	POLR2A	chr3:160938673-160939468	GM12892	blood:	n/a	n/a
10	FOXA1	chr3:160938786-160939189	T-47D	breast:	n/a	n/a
11	ZBTB33	chr3:160938804-160939261	GM12878	blood:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
12	TCF12	chr3:160938802-160939330	GM12878	blood:	n/a	n/a
13	MXI1	chr3:160938485-160940211	IMR90	lung:	n/a	n/a
14	POLR2A	chr3:160938785-160939545	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:160938604-160939422	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr3:160938739-160939332	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:160938727-160939893	HepG2	liver:	n/a	n/a
18	ELF1	chr3:160938677-160939711	MCF-7	breast:	n/a	chr3:160939264-160939276
19	MAX	chr3:160938417-160939855	A549	lung:	n/a	n/a
20	JUN	chr3:160938488-160939172	K562	blood:	n/a	chr3:160938885-160938899
21	POLR2A	chr3:160938710-160939508	GM12891	blood:	n/a	n/a
22	ZBTB33	chr3:160938732-160939387	A549	lung:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
23	POLR2A	chr3:160938583-160939595	K562	blood:	n/a	n/a
24	POLR2A	chr3:160938617-160939716	PBDE	blood:	n/a	n/a
25	GTF2F1	chr3:160938560-160939306	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:160938803-160939385	GM12892	blood:	n/a	n/a
27	NR2F2	chr3:160938686-160939722	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:160938760-160939613	GM18526	blood:	n/a	n/a
29	POLR2A	chr3:160938665-160939617	GM12891	blood:	n/a	n/a
30	WRNIP1	chr3:160938567-160939119	GM12878	blood:	n/a	n/a
31	RUNX3	chr3:160938752-160939617	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:160938587-160939517	HUVEC	blood vessel:	n/a	n/a
33	MYC	chr3:160938669-160939615	K562	blood:	n/a	n/a
34	POLR2A	chr3:160938663-160939412	GM12878	blood:	n/a	n/a
35	TAF1	chr3:160938796-160939462	K562	blood:	n/a	n/a
36	POLR2A	chr3:160938714-160939262	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:160938744-160939487	HCT-116	colon:	n/a	n/a
38	POLR2A	chr3:160938514-160939703	K562	blood:	n/a	n/a
39	TAF1	chr3:160938647-160939465	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr3:160938538-160939600	ProgFib	skin:	n/a	n/a
41	POLR2A	chr3:160938668-160939572	HCT-116	colon:	n/a	n/a
42	POLR2A	chr3:160938716-160939371	HepG2	liver:	n/a	n/a
43	ATF2	chr3:160938720-160939412	GM12878	blood:	n/a	n/a
44	HEY1	chr3:160938792-160939269	HepG2	liver:	n/a	n/a
45	CUX1	chr3:160938792-160939242	GM12878	blood:	n/a	n/a
46	TCF12	chr3:160938782-160939573	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr3:160938613-160939632	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:160938618-160940054	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:160938635-160939619	HL-60	blood:	n/a	n/a
50	YY1	chr3:160938787-160939432	SK-N-SH_RA	brain:	n/a	chr3:160939248-160939262

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160937993..160941056-chr3:161047965..161051023,3	MCF-7	breast:
2	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
3	chr19:12902198..12902786-chr3:160938697..160939572,2	Hela-S3	cervix:
4	chr11:74459661..74460383-chr3:160938597..160939219,2	Hela-S3	cervix:
5	chr3:160938091..160940577-chr7:104653089..104654973,2	MCF-7	breast:
6	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
7	chr12:123319135..123321319-chr3:160936978..160939441,2	MCF-7	breast:
8	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
9	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
10	chr3:160938062..160938917-chr4:54930258..54930848,2	Hela-S3	cervix:
11	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:

No data

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000109220	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000166439	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12488037	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488318	0.91[ASN][1000 genomes]
rs12494261	0.92[ASN][1000 genomes]
rs12494844	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13318781	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13320863	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471440	0.86[ASN][1000 genomes]
rs1478567	0.92[ASN][1000 genomes]
rs1599380	0.80[AMR][1000 genomes]
rs1599391	0.85[EUR][1000 genomes]
rs163138	0.80[ASN][1000 genomes]
rs1947685	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1970834	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs336544	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs336545	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs336546	0.84[ASN][1000 genomes]
rs336564	0.80[ASN][1000 genomes]
rs336565	0.80[ASN][1000 genomes]
rs336566	0.80[ASN][1000 genomes]
rs336581	0.80[ASN][1000 genomes]
rs336584	0.80[ASN][1000 genomes]
rs336587	0.80[ASN][1000 genomes]
rs336588	0.80[ASN][1000 genomes]
rs336592	0.80[ASN][1000 genomes]
rs35152606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35446590	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36105583	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4270539	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4429651	0.99[ASN][1000 genomes]
rs4487256	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4490410	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57201455	0.86[ASN][1000 genomes]
rs62278031	0.83[ASN][1000 genomes]
rs62279860	0.99[ASN][1000 genomes]
rs62279861	0.99[ASN][1000 genomes]
rs62279862	0.97[ASN][1000 genomes]
rs6799805	0.80[ASN][1000 genomes]
rs731363	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73160351	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73160362	0.99[ASN][1000 genomes]
rs73162530	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7622060	0.80[ASN][1000 genomes]
rs7649959	0.80[ASN][1000 genomes]
rs9290067	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9290068	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9290072	0.92[ASN][1000 genomes]
rs9290075	0.91[ASN][1000 genomes]
rs978933	0.86[ASN][1000 genomes]
rs9810737	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9811833	0.87[ASN][1000 genomes]
rs9812083	0.92[ASN][1000 genomes]
rs9818516	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9824501	0.85[EUR][1000 genomes]
rs9825118	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9827833	0.89[ASN][1000 genomes]
rs9828189	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9828205	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9828231	0.97[ASN][1000 genomes]
rs9831725	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9836074	0.85[EUR][1000 genomes]
rs9836094	0.99[ASN][1000 genomes]
rs9839404	0.92[ASN][1000 genomes]
rs9842281	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9857946	0.92[ASN][1000 genomes]
rs9858399	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9859045	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9862258	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9876553	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9878365	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62278055	DNMT1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160933200-160939000	Weak transcription	Gastric	stomach
2	chr3:160938000-160940400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr3:160938200-160940400	Active TSS	A549	lung
4	chr3:160938200-160940600	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:160938200-160940600	Active TSS	Brain Hippocampus Middle	brain
6	chr3:160938200-160940600	Active TSS	Right Atrium	heart
7	chr3:160938200-160940600	Active TSS	Thymus	Thymus
8	chr3:160938200-160940600	Active TSS	HSMM	muscle
9	chr3:160938400-160939000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:160938400-160939000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:160938400-160939000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr3:160938400-160939000	Flanking Active TSS	NHEK	skin
13	chr3:160938400-160939200	Active TSS	Fetal Brain Female	brain
14	chr3:160938400-160939600	Active TSS	Primary B cells from cord blood	blood
15	chr3:160938400-160939800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr3:160938400-160940000	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:160938400-160940400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:160938400-160940400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:160938400-160940400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:160938400-160940600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:160938400-160940600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr3:160938400-160940600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:160938400-160940600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:160938400-160940600	Active TSS	GM12878-XiMat	blood
25	chr3:160938400-160940600	Active TSS	NH-A	brain
26	chr3:160938400-160940800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:160938400-160941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:160938400-160941400	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr3:160938400-160941600	Active TSS	Stomach Smooth Muscle	stomach
30	chr3:160938600-160939000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr3:160938600-160939000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr3:160938600-160939000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr3:160938600-160939000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:160938600-160939000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:160938600-160939000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:160938600-160939200	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr3:160938600-160939200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:160938600-160939400	Active TSS	HepG2	liver
39	chr3:160938600-160939800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:160938600-160939800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:160938600-160940000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:160938600-160940000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:160938600-160940000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:160938600-160940000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr3:160938600-160940200	Active TSS	Placenta	Placenta
46	chr3:160938600-160940400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:160938600-160940400	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr3:160938600-160940400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:160938600-160940400	Active TSS	Brain Angular Gyrus	brain
50	chr3:160938600-160940600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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