Variant report

Variant	rs3738317
Chromosome Location	chr1:47898461-47898462
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:95)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:95 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:47898068-47898503	MCF-7	breast:	n/a	n/a
2	YY1	chr1:47898138-47898465	K562	blood:	n/a	n/a
3	RAD21	chr1:47898005-47898479	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:47898084-47898477	K562	blood:	n/a	n/a
5	BACH1	chr1:47897997-47898794	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr1:47898085-47898548	K562	blood:	n/a	n/a
7	BRCA1	chr1:47898058-47898469	GM12878	blood:	n/a	n/a
8	MAX	chr1:47898124-47898636	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:47897846-47898496	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr1:47898264-47898701	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:47897237-47899005	MCF10A-Er-Src	breast:	n/a	n/a
12	SMC3	chr1:47897989-47898542	GM12878	blood:	n/a	n/a
13	CHD2	chr1:47898122-47898926	GM12878	blood:	n/a	n/a
14	BRCA1	chr1:47898054-47898565	H1-hESC	embryonic stem cell:	n/a	n/a
15	EBF1	chr1:47898153-47898670	GM12878	blood:	n/a	n/a
16	RAD21	chr1:47898059-47898487	H1-hESC	embryonic stem cell:	n/a	n/a
17	NR2F2	chr1:47897985-47898568	K562	blood:	n/a	n/a
18	RAD21	chr1:47898084-47898531	A549	lung:	n/a	n/a
19	ZNF263	chr1:47898071-47898644	HEK293-T-REx	kidney:	n/a	n/a
20	HMGN3	chr1:47898264-47898670	K562	blood:	n/a	n/a
21	CTCF	chr1:47898117-47898695	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr1:47898027-47898469	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:47897950-47898468	IMR90	lung:	n/a	n/a
24	SMC3	chr1:47897848-47899184	SK-N-SH	brain:	n/a	n/a
25	GABPA	chr1:47898032-47898617	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr1:47897388-47899290	SK-N-SH	brain:	n/a	n/a
27	RFX5	chr1:47898412-47898573	H1-hESC	embryonic stem cell:	n/a	n/a
28	SUZ12	chr1:47898147-47900955	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr1:47898440-47898590	GM12874	blood:	n/a	n/a
30	MAX	chr1:47897911-47898474	K562	blood:	n/a	n/a
31	CBX3	chr1:47897810-47898473	K562	blood:	n/a	n/a
32	RAD21	chr1:47897791-47899034	SK-N-SH	brain:	n/a	n/a
33	MAX	chr1:47898127-47898646	GM12878	blood:	n/a	n/a
34	EP300	chr1:47897827-47898483	GM12878	blood:	n/a	n/a
35	CTCF	chr1:47897890-47898601	A549	lung:	n/a	n/a
36	RAD21	chr1:47898009-47898483	HepG2	liver:	n/a	n/a
37	MYC	chr1:47897745-47898495	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr1:47898447-47898651	Pancreas_OC	pancreas:	n/a	n/a
39	POLR2A	chr1:47898092-47898521	H1-neurons	neurons:	n/a	n/a
40	MYC	chr1:47898416-47898573	MCF-7	breast:	n/a	n/a
41	RAD21	chr1:47898049-47898609	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr1:47898428-47898694	GM12878	blood:	n/a	n/a
43	ELF1	chr1:47898130-47898931	GM12878	blood:	n/a	n/a
44	MYC	chr1:47897574-47898467	NB4	blood:	n/a	n/a
45	BHLHE40	chr1:47897979-47898563	GM12878	blood:	n/a	n/a
46	CTCF	chr1:47898460-47898610	GM12875	blood:	n/a	n/a
47	CTCF	chr1:47898453-47898683	GM19240	blood:	n/a	n/a
48	YY1	chr1:47897999-47898537	H1-hESC	embryonic stem cell:	n/a	n/a
49	HCFC1	chr1:47898074-47898496	K562	blood:	n/a	n/a
50	KAP1	chr1:47898103-47898549	HEK293	kidney:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:47898435-47898485	ovcar-3	ovarian:	n/a
2	chr1:47898435-47898485	Hela-S3	cervix:	n/a
3	chr1:47898435-47898485	AG09309	skin:	n/a
4	chr1:47898435-47898485	SAEC	small airway:	n/a
5	chr1:47898435-47898485	ProgFib	skin:	n/a
6	chr1:47898435-47898485	HL-60	blood:	n/a
7	chr1:47898435-47898485	HRPEpiC	eye:	n/a
8	chr1:47898435-47898485	PFSK-1	brain:	n/a
9	chr1:47898435-47898485	IMR90	lung:	fetal
10	chr1:47898435-47898485	Hepatocyte	liver:	n/a
11	chr1:47898435-47898485	SK-N-MC	brain:	n/a
12	chr1:47898435-47898485	HRCEpiC	kidney:	n/a
13	chr1:47898435-47898485	AG09319	gingival:	n/a
14	chr1:47898435-47898485	AG10803	skin:	n/a
15	chr1:47898435-47898485	K562	blood:	n/a
16	chr1:47898435-47898485	Jurkat	blood:	n/a
17	chr1:47898435-47898485	T-47D	breast:	n/a
18	chr1:47898435-47898485	AG04450	lung:	fetal
19	chr1:47898435-47898485	H1-hESC	embryonic stem cell:	embryo
20	chr1:47898435-47898485	HCPEpiC	choroid plexus:	n/a
21	chr1:47898435-47898485	HUVEC	blood vessel:	n/a
22	chr1:47898435-47898485	NHBE	bronchial:	n/a
23	chr1:47898435-47898485	NB4	blood:	n/a
24	chr1:47898435-47898485	HAEpiC	amniotic membrane:	n/a
25	chr1:47898435-47898485	HEEpiC	esophagus:	n/a
26	chr1:47898435-47898485	HMEC	breast:	n/a
27	chr1:47898435-47898485	HCM	heart:	n/a
28	chr1:47898435-47898485	NT2-D1	testis:	n/a
29	chr1:47898435-47898485	RPTEC	kidney:	n/a
30	chr1:47898435-47898485	ECC-1	luminal epithelium:	n/a
31	chr1:47898435-47898485	HIPEpiC	eye:	n/a
32	chr1:47898435-47898485	CMK	blood:	n/a
33	chr1:47898435-47898485	PANC-1	pancreas:	n/a
34	chr1:47898435-47898485	GM12892	blood:	n/a
35	chr1:47898435-47898485	A549	lung:	n/a
36	chr1:47898435-47898485	NH-A	brain:	n/a
37	chr1:47898435-47898485	GM12878	blood:	n/a
38	chr1:47898435-47898485	MCF-7	breast:	n/a
39	chr1:47898435-47898485	SK-N-SH_RA	brain:	n/a
40	chr1:47898435-47898485	HRE	kidney:	n/a
41	chr1:47898435-47898485	Caco-2	colon:	n/a
42	chr1:47898435-47898485	GM12891	blood:	n/a
43	chr1:47898435-47898485	GM19239	blood:	n/a
44	chr1:47898435-47898485	LNCaP	prostate:	n/a
45	chr1:47898435-47898485	HepG2	liver:	n/a
46	chr1:47898435-47898485	HCT-116	colon:	n/a
47	chr1:47898435-47898485	AG04449	skin:	fetal
48	chr1:47898435-47898485	AoSMC	blood vessel:	n/a
49	chr1:47898435-47898485	HNPCEpiC	eye:	n/a
50	chr1:47898435-47898485	BJ	skin:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47897936..47898688-chr1:48191191..48192530,4	MCF-7	breast:
2	chr1:47897306..47899124-chr1:48175410..48177072,8	MCF-7	breast:
3	chr1:47897729..47898695-chr1:48191656..48192720,4	K562	blood:
4	chr1:47896953..47898779-chr1:47905592..47907484,2	K562	blood:
5	chr1:47897740..47898693-chr1:47957289..47957863,2	K562	blood:
6	chr1:47897313..47899575-chr1:48174901..48176942,2	K562	blood:
7	chr1:47656064..47657895-chr1:47897057..47898698,2	K562	blood:
8	chr1:47897798..47898690-chr1:48175909..48176809,4	K562	blood:
9	chr1:47898149..47898683-chr1:47980817..47981372,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIL-2	chr1:47897805-47900313	ENSG00000237424.1
2	lnc-STIL-2	chr1:47897807-47900313	NR_026878

No data

Variant related genes	Relation type
FOXD2	TF binding region
FOXD2	CpG island
ENSG00000162366	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11211529	1.00[EUR][1000 genomes]
rs11211536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12021515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12026379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12032801	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12049416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1680019	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17103177	1.00[EUR][1000 genomes]
rs17103179	1.00[EUR][1000 genomes]
rs17103196	1.00[EUR][1000 genomes]
rs1765156	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1813427	1.00[EUR][1000 genomes]
rs2253511	1.00[EUR][1000 genomes]
rs2506984	1.00[EUR][1000 genomes]
rs2622906	1.00[EUR][1000 genomes]
rs2622911	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4926868	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs495482	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs506329	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs522768	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs527430	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs557101	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60042036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs642750	1.00[EUR][1000 genomes]
rs6683513	0.87[EUR][1000 genomes]
rs6688278	0.87[EUR][1000 genomes]
rs66904716	1.00[EUR][1000 genomes]
rs6703935	1.00[EUR][1000 genomes]
rs693036	1.00[EUR][1000 genomes]
rs72480616	1.00[EUR][1000 genomes]
rs72553947	1.00[EUR][1000 genomes]
rs72553949	1.00[EUR][1000 genomes]
rs72637985	0.87[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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47894400-47901600	Weak transcription	HepG2	liver
2	chr1:47896800-47900600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr1:47897000-47900200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:47897000-47901600	Weak transcription	A549	lung
5	chr1:47897200-47898600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:47897200-47898800	Enhancers	K562	blood
7	chr1:47897200-47899200	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:47897200-47899800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr1:47897200-47900400	Enhancers	Liver	Liver
10	chr1:47897200-47900600	Bivalent Enhancer	Fetal Stomach	stomach
11	chr1:47897400-47898800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:47897400-47898800	Enhancers	Spleen	Spleen
13	chr1:47897600-47898600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr1:47897600-47898800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:47897600-47899000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
16	chr1:47897600-47899000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
17	chr1:47897600-47899400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:47897600-47900200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:47897600-47900400	Bivalent Enhancer	Fetal Thymus	thymus
20	chr1:47897800-47898600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:47897800-47898600	Bivalent Enhancer	Left Ventricle	heart
22	chr1:47897800-47898600	Enhancers	Pancreas	Pancrea
23	chr1:47897800-47898800	Flanking Active TSS	HSMM	muscle
24	chr1:47897800-47899000	Strong transcription	Dnd41	blood
25	chr1:47897800-47899200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:47897800-47899400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:47897800-47900200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:47897800-47900400	Bivalent Enhancer	Fetal Heart	heart
29	chr1:47898000-47898600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr1:47898000-47898600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
31	chr1:47898000-47898600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
32	chr1:47898000-47898600	Flanking Active TSS	HSMMtube	muscle
33	chr1:47898000-47898600	Flanking Active TSS	Osteobl	bone
34	chr1:47898000-47898800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:47898000-47898800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
36	chr1:47898000-47898800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:47898000-47898800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:47898000-47898800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:47898000-47898800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr1:47898000-47899000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr1:47898000-47899000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:47898000-47899200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
43	chr1:47898000-47899200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
44	chr1:47898000-47900000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr1:47898000-47900200	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr1:47898000-47900400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
47	chr1:47898000-47900400	Flanking Active TSS	HMEC	breast
48	chr1:47898000-47900600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:47898200-47898600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:47898200-47898600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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