Variant report

Variant	rs7596302
Chromosome Location	chr2:72377841-72377842
allele	C/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	SMC3	chr2:72376645-72378392	SK-N-SH	brain:	n/a	chr2:72377064-72377078 chr2:72378074-72378088
2	RAD21	chr2:72377237-72378324	MCF-7	breast:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
3	SP1	chr2:72377148-72377950	A549	lung:	n/a	chr2:72377322-72377336
4	RAD21	chr2:72377030-72378384	A549	lung:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
5	RAD21	chr2:72377230-72378285	SK-N-SH_RA	brain:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
6	RCOR1	chr2:72377465-72377887	K562	blood:	n/a	n/a
7	RAD21	chr2:72377227-72378237	ECC-1	luminal epithelium:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
8	RAD21	chr2:72377287-72378246	HepG2	liver:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
9	SP1	chr2:72377268-72377899	A549	lung:	n/a	chr2:72377322-72377336
10	CTCF	chr2:72377444-72378098	K562	blood:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72377658-72377667 chr2:72378073-72378089
11	SMC3	chr2:72377252-72378131	HepG2	liver:	n/a	chr2:72378074-72378088
12	RAD21	chr2:72377347-72378118	HepG2	liver:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
13	CTCF	chr2:72377351-72377971	MCF-7	breast:	n/a	chr2:72377658-72377667
14	RAD21	chr2:72376829-72378435	SK-N-SH	brain:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
15	RAD21	chr2:72377271-72378202	H1-hESC	embryonic stem cell:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
16	MAX	chr2:72371598-72378199	A549	lung:	n/a	chr2:72377135-72377144 chr2:72372838-72372848 chr2:72372537-72372547 chr2:72374470-72374480 chr2:72375058-72375068 chr2:72376080-72376090 chr2:72374306-72374316
17	MAZ	chr2:72377300-72377990	K562	blood:	n/a	n/a
18	CTCF	chr2:72377171-72378368	HCT-116	colon:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72377658-72377667 chr2:72378073-72378089
19	ZNF143	chr2:72377488-72377841	Hela-S3	cervix:	n/a	n/a
20	SMC3	chr2:72377444-72377852	K562	blood:	n/a	n/a
21	CTCF	chr2:72377474-72377846	GM12892	blood:	n/a	chr2:72377658-72377667
22	RAD21	chr2:72377313-72378187	A549	lung:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
23	BHLHE40	chr2:72377386-72377945	K562	blood:	n/a	n/a
24	RAD21	chr2:72377178-72378372	HCT-116	colon:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
25	MAZ	chr2:72377484-72377888	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr2:72377367-72378244	HepG2	liver:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72377658-72377667 chr2:72378073-72378089
27	CHD2	chr2:72377512-72377863	HepG2	liver:	n/a	n/a
28	CTCF	chr2:72376337-72378708	A549	lung:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72376587-72376600 chr2:72377658-72377667 chr2:72378073-72378089 chr2:72377065-72377078
29	RAD21	chr2:72377267-72378340	A549	lung:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
30	CTCF	chr2:72377331-72377938	A549	lung:	n/a	chr2:72377658-72377667
31	POLR2A	chr2:72377078-72377895	Hela-S3	cervix:	n/a	n/a
32	BCL3	chr2:72376921-72378279	A549	lung:	n/a	chr2:72376958-72376971
33	FOXA2	chr2:72376757-72377843	A549	lung:	n/a	n/a
34	CTCF	chr2:72377424-72377845	A549	lung:	n/a	chr2:72377658-72377667
35	RAD21	chr2:72377169-72378285	MCF-7	breast:	n/a	chr2:72378073-72378092 chr2:72377659-72377668
36	TCF12	chr2:72375012-72378329	A549	lung:	n/a	chr2:72377118-72377125 chr2:72377018-72377027 chr2:72377343-72377353
37	RAD21	chr2:72377450-72377844	GM12878	blood:	n/a	chr2:72377659-72377668
38	ELK1	chr2:72377636-72377953	K562	blood:	n/a	n/a
39	SMC3	chr2:72377311-72378284	Hela-S3	cervix:	n/a	chr2:72378074-72378088
40	RAD21	chr2:72377112-72378071	IMR90	lung:	n/a	chr2:72377659-72377668
41	RFX5	chr2:72377462-72378103	Hela-S3	cervix:	n/a	n/a
42	CREB1	chr2:72377410-72377856	A549	lung:	n/a	n/a
43	RAD21	chr2:72377453-72377875	H1-hESC	embryonic stem cell:	n/a	chr2:72377659-72377668
44	FOSL2	chr2:72377060-72378190	A549	lung:	n/a	n/a
45	CTCF	chr2:72377380-72377853	K562	blood:	n/a	chr2:72377658-72377667
46	RAD21	chr2:72377432-72377842	SK-N-SH_RA	brain:	n/a	chr2:72377659-72377668
47	CTCF	chr2:72376862-72378456	SK-N-SH	brain:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72377658-72377667 chr2:72378073-72378089 chr2:72377065-72377078
48	MAX	chr2:72375789-72377858	A549	lung:	n/a	chr2:72377135-72377144 chr2:72376080-72376090
49	SMC3	chr2:72377387-72377861	GM12878	blood:	n/a	n/a
50	CTCF	chr2:72377478-72378115	GM19238	blood:	n/a	chr2:72378072-72378090 chr2:72378074-72378095 chr2:72377658-72377667 chr2:72378073-72378089

No.	Distal block	Cell Line	Cell type
1	chr2:71775514..71776291-chr2:72377222..72378256,3	MCF-7	breast:
2	chr2:72377559..72378350-chr2:72552758..72553572,2	MCF-7	breast:
3	chr2:72373378..72375248-chr2:72375782..72378239,2	K562	blood:
4	chr2:71757981..71758516-chr2:72377608..72378139,2	K562	blood:
5	chr2:72377794..72378536-chr2:72552704..72553708,5	MCF-7	breast:
6	chr2:72377204..72379877-chr2:72380463..72383459,3	MCF-7	breast:
7	chr2:72377620..72378560-chr2:72972635..72973309,3	MCF-7	breast:
8	chr2:72028908..72029874-chr2:72377185..72378148,5	K562	blood:
9	chr2:72377339..72378675-chr2:72806432..72807386,5	MCF-7	breast:
10	chr2:72377572..72378539-chr2:72594368..72595601,4	MCF-7	breast:
11	chr2:72342481..72343002-chr2:72377243..72378029,2	MCF-7	breast:
12	chr2:72150758..72151644-chr2:72377122..72377984,3	MCF-7	breast:
13	chr2:72150816..72151705-chr2:72377178..72378139,6	MCF-7	breast:
14	chr2:72368510..72373839-chr2:72374615..72379122,7	MCF-7	breast:
15	chr2:72160749..72161681-chr2:72377188..72378098,6	MCF-7	breast:
16	chr2:72098804..72099311-chr2:72377199..72378032,2	MCF-7	breast:
17	chr2:72150800..72151677-chr2:72377276..72378106,3	K562	blood:
18	chr2:71775510..71776018-chr2:72377254..72377932,2	MCF-7	breast:
19	chr2:71775478..71776768-chr2:72377188..72378065,4	K562	blood:
20	chr2:72376084..72377923-chr2:72805455..72808072,2	K562	blood:
21	chr2:72222448..72223171-chr2:72377349..72378216,3	MCF-7	breast:

Variant related genes	Relation type
CYP26B1	TF binding region
ENSG00000003137	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1002415	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs10166057	0.89[ASN][1000 genomes]
rs10171231	0.87[CEU][hapmap]
rs10202129	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10490039	0.87[CEU][hapmap]
rs10490040	0.87[CEU][hapmap]
rs13339845	0.87[CEU][hapmap]
rs13407599	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17007927	0.87[CEU][hapmap]
rs17007929	0.87[CEU][hapmap]
rs17007933	0.87[CEU][hapmap]
rs17007934	0.87[CEU][hapmap]
rs17007937	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs2192012	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs2901091	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768638	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3768639	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3768641	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs62150093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150094	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62150096	0.92[EUR][1000 genomes]
rs6546745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546748	0.96[ASN][1000 genomes]
rs6705261	0.86[CEU][hapmap]
rs6705347	0.86[CEU][hapmap]
rs6710195	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6710373	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738598	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738942	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748698	0.87[CEU][hapmap]
rs7557210	0.89[ASN][1000 genomes]
rs9309462	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[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	nsv582207	chr2:72329603-72389334	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription 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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72375800-72378000	Flanking Bivalent TSS/Enh	HepG2	liver
2	chr2:72376200-72378000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:72376200-72378000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
4	chr2:72376400-72378000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
5	chr2:72376600-72378000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:72376600-72378000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr2:72376600-72378000	Enhancers	Liver	Liver
8	chr2:72376600-72378000	Enhancers	Lung	lung
9	chr2:72376800-72378000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:72376800-72378000	Bivalent Enhancer	Placenta	Placenta
11	chr2:72377200-72378000	Bivalent Enhancer	Left Ventricle	heart
12	chr2:72377400-72378000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:72377400-72378000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr2:72377400-72378000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:72377600-72378000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr2:72377600-72378000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr2:72377600-72378000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr2:72377600-72378000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:72377600-72378000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:72377600-72378000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:72377600-72378000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr2:72377600-72378000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
23	chr2:72377600-72378000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
24	chr2:72377600-72378000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr2:72377600-72378000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:72377600-72378000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:72377600-72378000	Bivalent Enhancer	Adipose Nuclei	Adipose
28	chr2:72377600-72378000	Enhancers	Brain Hippocampus Middle	brain
29	chr2:72377600-72378000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
30	chr2:72377600-72378000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:72377600-72378000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
32	chr2:72377600-72378000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr2:72377600-72378000	Bivalent Enhancer	Fetal Brain Male	brain
34	chr2:72377600-72378000	Enhancers	Fetal Heart	heart
35	chr2:72377600-72378000	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr2:72377600-72378000	Bivalent Enhancer	Fetal Lung	lung
37	chr2:72377600-72378000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr2:72377600-72378000	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr2:72377600-72378000	Bivalent Enhancer	Fetal Stomach	stomach
40	chr2:72377600-72378000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
41	chr2:72377600-72378000	Enhancers	Spleen	Spleen
42	chr2:72377600-72378200	Bivalent Enhancer	Brain Substantia Nigra	brain
43	chr2:72377600-72378200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
44	chr2:72377600-72381400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:72377800-72378000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:72377800-72378000	Bivalent Enhancer	Colon Smooth Muscle	Colon
47	chr2:72377800-72378000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr2:72377800-72378000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
49	chr2:72377800-72378000	Flanking Bivalent TSS/Enh	A549	lung
50	chr2:72377800-72378000	Active TSS	Hela-S3	cervix

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