Variant report

Variant	rs28491609
Chromosome Location	chr15:78292743-78292744
allele	C/T
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	CTCF	chr15:78292420-78292744	GM12892	blood:	n/a	chr15:78292671-78292684
2	POLR2A	chr15:78292562-78292840	HL-60	blood:	n/a	n/a
3	CTCF	chr15:78292400-78292750	Spleen_OC	spleen:	n/a	chr15:78292671-78292684
4	RAD21	chr15:78292315-78292816	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr15:78292164-78293053	A549	lung:	n/a	chr15:78292671-78292684
6	RAD21	chr15:78292229-78292902	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr15:78292391-78292903	HCT-116	colon:	n/a	n/a
8	RAD21	chr15:78292382-78292757	HepG2	liver:	n/a	n/a
9	CTCF	chr15:78292371-78292751	T-47D	breast:	n/a	chr15:78292671-78292684
10	MAZ	chr15:78292431-78292767	K562	blood:	n/a	chr15:78292598-78292608
11	RAD21	chr15:78292335-78292747	A549	lung:	n/a	n/a
12	SP4	chr15:78292367-78292751	H1-hESC	embryonic stem cell:	n/a	chr15:78292595-78292611 chr15:78292649-78292665 chr15:78292651-78292667 chr15:78292597-78292608
13	GABPA	chr15:78292329-78292795	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr15:78292331-78292791	GM12878	blood:	n/a	chr15:78292598-78292608 chr15:78292597-78292609 chr15:78292652-78292662 chr15:78292652-78292662 chr15:78292597-78292609 chr15:78292597-78292608
15	CTCF	chr15:78292383-78292747	HepG2	liver:	n/a	chr15:78292671-78292684
16	CTCF	chr15:78292359-78292790	A549	lung:	n/a	chr15:78292671-78292684
17	CTCF	chr15:78292252-78292774	A549	lung:	n/a	chr15:78292671-78292684
18	RAD21	chr15:78292436-78292844	MCF-7	breast:	n/a	n/a
19	RAD21	chr15:78292336-78292763	HepG2	liver:	n/a	n/a
20	CTCF	chr15:78292311-78292796	H1-hESC	embryonic stem cell:	n/a	chr15:78292671-78292684
21	POLR2A	chr15:78292381-78292852	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr15:78292551-78292801	HCT-116	colon:	n/a	n/a
23	CTCF	chr15:78292344-78292775	K562	blood:	n/a	chr15:78292671-78292684
24	CHD2	chr15:78292621-78292765	GM12878	blood:	n/a	n/a
25	RAD21	chr15:78292386-78292818	GM12878	blood:	n/a	n/a
26	CTCF	chr15:78292405-78292759	GM19240	blood:	n/a	chr15:78292671-78292684
27	CTCF	chr15:78292257-78292804	H1-hESC	embryonic stem cell:	n/a	chr15:78292671-78292684
28	EBF1	chr15:78292457-78292779	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:78292572-78292768	A549	lung:	n/a	n/a
30	CTCF	chr15:78292343-78292825	K562	blood:	n/a	chr15:78292671-78292684
31	FOXM1	chr15:78292344-78292769	GM12878	blood:	n/a	n/a
32	RAD21	chr15:78292391-78292851	ECC-1	luminal epithelium:	n/a	n/a
33	RAD21	chr15:78292403-78292859	A549	lung:	n/a	n/a
34	CTCF	chr15:78292396-78292877	MCF-7	breast:	n/a	chr15:78292671-78292684
35	CTCF	chr15:78292185-78293134	SK-N-SH	brain:	n/a	chr15:78292671-78292684
36	POLR2A	chr15:78292527-78292804	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr15:78292365-78292757	GM12878	blood:	n/a	chr15:78292671-78292684
38	POLR2A	chr15:78292593-78292857	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr15:78292577-78292898	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr15:78292492-78292896	Hela-S3	cervix:	n/a	n/a
41	RAD21	chr15:78292399-78292843	MCF-7	breast:	n/a	n/a
42	SP4	chr15:78292320-78292855	H1-hESC	embryonic stem cell:	n/a	chr15:78292595-78292611 chr15:78292649-78292665 chr15:78292651-78292667 chr15:78292597-78292608
43	RAD21	chr15:78292336-78292822	HepG2	liver:	n/a	n/a
44	RAD21	chr15:78292385-78292915	HCT-116	colon:	n/a	n/a
45	TCF3	chr15:78292449-78292792	GM12878	blood:	n/a	chr15:78292487-78292503 chr15:78292491-78292500
46	RAD21	chr15:78292384-78292863	ECC-1	luminal epithelium:	n/a	n/a
47	TEAD4	chr15:78292388-78292780	H1-hESC	embryonic stem cell:	n/a	n/a
48	CREB1	chr15:78292415-78292749	A549	lung:	n/a	n/a
49	NFIC	chr15:78292453-78292831	ECC-1	luminal epithelium:	n/a	n/a
50	YY1	chr15:78292300-78292855	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78292248..78292748-chr15:79043024..79043675,2	Hela-S3	cervix:
2	chr15:78290955..78292806-chr15:79043518..79045037,2	MCF-7	breast:
3	chr15:78292050..78293044-chr15:78400416..78401371,3	K562	blood:
4	chr15:78292459..78292975-chr15:79043082..79043688,2	HCT-116	colon:
5	chr15:78292129..78292970-chr15:78533019..78533578,2	K562	blood:
6	chr15:78251300..78252464-chr15:78292151..78292856,3	MCF-7	breast:
7	chr15:78258912..78259522-chr15:78292151..78292959,2	MCF-7	breast:
8	chr15:78291946..78293315-chr15:78400365..78401521,34	MCF-7	breast:
9	chr15:78291849..78292957-chr15:79043056..79044329,6	K562	blood:
10	chr15:78290983..78293923-chr15:78293965..78296117,2	MCF-7	breast:
11	chr15:78292246..78292984-chr15:79043169..79044003,5	MCF-7	breast:
12	chr15:78292186..78292985-chr15:79043320..79043997,6	MCF-7	breast:
13	chr15:78292095..78293104-chr15:78399979..78401592,9	MCF-7	breast:
14	chr15:78292154..78293026-chr15:78401681..78402212,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D2B	TF binding region
ENSG00000167202	Chromatin interaction
ENSG00000238166	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10519182	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12102130	0.88[AFR][1000 genomes]
rs13329101	0.88[AFR][1000 genomes]
rs13329302	0.88[AFR][1000 genomes]
rs16969405	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16969407	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16969408	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16969414	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16969424	0.88[AFR][1000 genomes]
rs16969430	0.88[AFR][1000 genomes]
rs1985487	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28417785	0.88[AFR][1000 genomes]
rs28441175	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28451835	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28470811	0.94[EUR][1000 genomes]
rs28491820	0.88[AFR][1000 genomes]
rs28526757	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28579273	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28581571	0.92[AFR][1000 genomes]
rs28591625	0.88[AFR][1000 genomes]
rs28647720	0.92[AFR][1000 genomes]
rs28674965	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4991997	0.83[EUR][1000 genomes]
rs55663439	0.83[EUR][1000 genomes]
rs55930913	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs58098690	0.83[EUR][1000 genomes]
rs58117418	0.83[EUR][1000 genomes]
rs7167778	0.94[EUR][1000 genomes]
rs74027705	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs74027706	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs74027709	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs74029743	0.83[EUR][1000 genomes]
rs74029754	0.94[EUR][1000 genomes]
rs7495639	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9920647	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78280200-78295800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:78283400-78292800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:78283400-78293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:78283400-78296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:78283400-78305000	Weak transcription	K562	blood
6	chr15:78283600-78294800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:78283600-78300800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:78283800-78301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:78284800-78296400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:78285400-78295800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:78285400-78304400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:78285800-78299200	Strong transcription	Fetal Intestine Large	intestine
14	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:78286400-78295200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:78286600-78293400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:78286600-78293400	Weak transcription	Small Intestine	intestine
19	chr15:78286600-78296400	Strong transcription	Fetal Intestine Small	intestine
20	chr15:78286800-78295200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:78287000-78293400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:78287600-78293400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:78287600-78295400	Weak transcription	Psoas Muscle	Psoas
25	chr15:78287800-78297400	Weak transcription	A549	lung
26	chr15:78288000-78294800	Weak transcription	HUVEC	blood vessel
27	chr15:78288200-78293000	Weak transcription	NH-A	brain
28	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:78288600-78297000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:78288600-78303000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:78288600-78304400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
36	chr15:78288800-78292800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:78288800-78292800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:78288800-78292800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:78288800-78293200	Genic enhancers	Fetal Muscle Leg	muscle
40	chr15:78288800-78295200	Weak transcription	HMEC	breast
41	chr15:78288800-78304800	Weak transcription	Fetal Kidney	kidney
42	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr15:78289000-78293200	Weak transcription	NHEK	skin
45	chr15:78289000-78295600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:78289000-78295800	Strong transcription	Brain Hippocampus Middle	brain
47	chr15:78289000-78309800	Strong transcription	Primary T cells from cord blood	blood
48	chr15:78289200-78293000	Strong transcription	Gastric	stomach
49	chr15:78289400-78293600	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr15:78289400-78294200	Strong transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links