Variant report

Variant	rs9848714
Chromosome Location	chr3:120004182-120004183
allele	A/G
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	GTF2F1	chr3:120004002-120004287	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr3:120003899-120004443	MCF-7	breast:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
3	POLR2A	chr3:120004072-120004557	SK-N-MC	brain:	n/a	n/a
4	E2F6	chr3:120003953-120004371	K562	blood:	n/a	chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
5	E2F6	chr3:120003943-120004365	A549	lung:	n/a	chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
6	CTCF	chr3:120004140-120004290	HUVEC	blood vessel:	n/a	n/a
7	MAX	chr3:120004006-120004420	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
8	TCF12	chr3:120003825-120004442	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr3:120004113-120004236	MCF-7	breast:	n/a	chr3:120004147-120004156
10	MYC	chr3:120003634-120004336	A549	lung:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
11	CTCF	chr3:120004100-120004250	SAEC	small airway:	n/a	n/a
12	MAX	chr3:120003992-120004367	A549	lung:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
13	CTCF	chr3:120004078-120004220	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:120004060-120004210	GM12867	blood:	n/a	n/a
15	HDAC2	chr3:120003731-120004236	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr3:120004067-120004189	K562	blood:	n/a	chr3:120004147-120004156
17	POLR2A	chr3:120003972-120004252	A549	lung:	n/a	n/a
18	MAX	chr3:120003672-120004472	ECC-1	luminal epithelium:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
19	CTCF	chr3:120004080-120004230	HMEC	breast:	n/a	n/a
20	CREB1	chr3:120003687-120004314	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr3:120003914-120004416	SK-N-SH	brain:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
22	CTCF	chr3:120004100-120004250	HCPEpiC	choroid plexus:	n/a	n/a
23	CTCF	chr3:120004102-120004186	MCF-7	breast:	n/a	n/a
24	MAX	chr3:120003778-120004530	ECC-1	luminal epithelium:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
25	MAX	chr3:120003986-120004353	HepG2	liver:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
26	MAX	chr3:120003833-120004535	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
27	POLR2A	chr3:120003842-120004306	H1-hESC	embryonic stem cell:	n/a	n/a
28	BRCA1	chr3:120004094-120004241	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr3:120004018-120004376	H1-hESC	embryonic stem cell:	n/a	chr3:120004124-120004134
30	MAX	chr3:120003825-120004548	H1-hESC	embryonic stem cell:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
31	E2F6	chr3:120003835-120004482	H1-hESC	embryonic stem cell:	n/a	chr3:120004378-120004388 chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
32	MAX	chr3:120004079-120004385	SK-N-SH	brain:	n/a	chr3:120004147-120004156
33	CTCF	chr3:120004060-120004210	HAc	cerebellar:	n/a	n/a
34	E2F6	chr3:120003973-120004304	K562	blood:	n/a	chr3:120004137-120004147 chr3:120004284-120004293 chr3:120004170-120004181
35	CREB1	chr3:120003858-120004261	K562	blood:	n/a	n/a
36	HMGN3	chr3:120004013-120004427	K562	blood:	n/a	n/a
37	HDAC2	chr3:120003685-120004370	MCF-7	breast:	n/a	n/a
38	CHD2	chr3:120004046-120004328	K562	blood:	n/a	chr3:120004124-120004134
39	CTCF	chr3:120004106-120004277	IMR90	lung:	n/a	n/a
40	MAX	chr3:120004026-120004245	K562	blood:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
41	TAF1	chr3:120003917-120004374	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZBTB7A	chr3:120003792-120004551	ECC-1	luminal epithelium:	n/a	chr3:120004339-120004346
43	MYC	chr3:120004181-120004190	MCF10A-Er-Src	breast:	n/a	n/a
44	MYC	chr3:120004004-120004246	MCF-7	breast:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
45	BACH1	chr3:120003519-120004298	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr3:120003882-120004487	MCF-7	breast:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
47	CTCF	chr3:120004074-120004197	Fibrobl	skin:	n/a	n/a
48	MXI1	chr3:120003847-120004521	IMR90	lung:	n/a	n/a
49	MAX	chr3:120003989-120004274	K562	blood:	n/a	chr3:120004147-120004156 chr3:120004041-120004051
50	POLR2A	chr3:120003840-120004342	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120002820..120005702-chr3:120066388..120068289,2	MCF-7	breast:

Variant related genes	Relation type
GPR156	TF binding region
ENSG00000163428	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10804551	0.84[EUR][1000 genomes]
rs10934526	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934527	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1118199	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11705881	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11706014	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707599	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12635156	0.84[EUR][1000 genomes]
rs12638442	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1388754	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1602613	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1873652	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1873653	0.88[ASN][1000 genomes]
rs2101657	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131176	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2319544	0.84[EUR][1000 genomes]
rs2319669	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319671	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319672	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4378995	0.94[ASN][1000 genomes]
rs6771865	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774960	0.94[ASN][1000 genomes]
rs6795868	0.94[ASN][1000 genomes]
rs72954789	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633690	0.84[EUR][1000 genomes]
rs9824334	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9833127	0.84[EUR][1000 genomes]
rs9843220	0.94[ASN][1000 genomes]
rs9849695	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856288	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9856618	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9858897	0.84[EUR][1000 genomes]
rs9875613	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120003000-120004600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:120003200-120004400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:120003200-120004400	Bivalent/Poised TSS	NHDF-Ad	bronchial
4	chr3:120003200-120004800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:120003400-120004200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:120003400-120004200	Bivalent/Poised TSS	Colonic Mucosa	Colon
7	chr3:120003400-120004200	Active TSS	NH-A	brain
8	chr3:120003400-120004400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:120003400-120004400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:120003400-120004400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
11	chr3:120003400-120004400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
12	chr3:120003400-120004400	Active TSS	Fetal Kidney	kidney
13	chr3:120003400-120004400	Enhancers	Lung	lung
14	chr3:120003400-120004400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr3:120003400-120004400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr3:120003400-120004400	Enhancers	Spleen	Spleen
17	chr3:120003400-120004600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:120003400-120004600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:120003400-120004600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:120003400-120004600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr3:120003400-120004600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:120003400-120004600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:120003400-120004600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
24	chr3:120003400-120004600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:120003400-120004600	Active TSS	Brain Substantia Nigra	brain
26	chr3:120003400-120004600	Active TSS	Colon Smooth Muscle	Colon
27	chr3:120003400-120004600	Active TSS	HSMM	muscle
28	chr3:120003400-120004600	Bivalent/Poised TSS	NHEK	skin
29	chr3:120003400-120004600	Bivalent/Poised TSS	Osteobl	bone
30	chr3:120003600-120004200	Active TSS	Brain Hippocampus Middle	brain
31	chr3:120003600-120004200	Active TSS	Esophagus	oesophagus
32	chr3:120003600-120004200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
33	chr3:120003600-120004200	Active TSS	Ovary	ovary
34	chr3:120003600-120004200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
35	chr3:120003600-120004200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
36	chr3:120003600-120004400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:120003600-120004400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr3:120003600-120004400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:120003600-120004400	Bivalent Enhancer	Liver	Liver
40	chr3:120003600-120004400	Active TSS	Brain Angular Gyrus	brain
41	chr3:120003600-120004400	Active TSS	Fetal Brain Female	brain
42	chr3:120003600-120004400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr3:120003600-120004400	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr3:120003600-120004400	Bivalent/Poised TSS	Left Ventricle	heart
45	chr3:120003600-120004400	Bivalent/Poised TSS	Thymus	Thymus
46	chr3:120003600-120004400	Active TSS	A549	lung
47	chr3:120003600-120004400	Active TSS	HSMMtube	muscle
48	chr3:120003600-120004600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr3:120003600-120004600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:120003600-120004600	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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